Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD check --install=check:Rgraphviz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Rgraphviz_2.54.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz.Rcheck’* using R version 4.5.0 (2025-04-11)* using platform: aarch64-unknown-linux-gnu* R was compiled by    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0    GNU Fortran (GCC) 14.2.0* running under: openEuler 24.03 (LTS)* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘Rgraphviz/DESCRIPTION’ ... OK* this is package ‘Rgraphviz’ version ‘2.54.0’* checking package namespace information ... OK* checking package dependencies ... OK* checking if this is a source package ... OK* checking if there is a namespace ... OK* checking for hidden files and directories ... OK* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘Rgraphviz’ can be installed ... WARNINGFound the following significant warnings:  dtdisc.c:13:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dthash.c:15:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dthash.c:81:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dtlist.c:11:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dtsize.c:11:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dtstat.c:11:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dtstat.c:31:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dttree.c:14:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dttreeset.c:11:18: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dtview.c:12:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]  dtwalk.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]  lexer.c:147:12: warning: pointer targets in returning 'unsigned char *' from a function with return type 'char *' differ in signedness [-Wpointer-sign]  lexer.c:435:33: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign]  lexer.c:435:41: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign]  route.c:107:29: warning: argument 4 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=]  shortest.c:103:47: warning: argument 2 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=]  trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]  BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses]  patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]See ‘/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz.Rcheck/00install.out’ for details.* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’* checking installed package size ... INFO  installed size is  5.4Mb  sub-directories of 1Mb or more:    libs   4.6Mb* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* checking top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking loading without being on the library search path ... OK* checking whether startup messages can be suppressed ... OK* checking dependencies in R code ... NOTEThere are ::: calls to the package's namespace in its code. A package  almost never needs to use ::: for its own objects:  ‘.graphviz_build_version’* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... OK* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTENon-topic package-anchored link(s) in Rd file 'layoutGraph.Rd':  ‘[graph:settings]{graph.par}’Non-topic package-anchored link(s) in Rd file 'renderGraph.Rd':  ‘[graph:settings]{graph.par}’See section 'Cross-references' in the 'Writing R Extensions' manual.* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking line endings in shell scripts ... OK* checking line endings in C/C++/Fortran sources/headers ... OK* checking line endings in Makefiles ... OK* checking compilation flags in Makevars ... OK* checking for GNU extensions in Makefiles ... OK* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK* checking use of PKG_*FLAGS in Makefiles ... OK* checking include directives in Makefiles ... OK* checking compiled code ... WARNINGNote: information on .o files is not availableFile ‘/home/biocbuild/R/R-4.5.0/site-library/Rgraphviz/libs/Rgraphviz.so’:  Found ‘abort’, possibly from ‘abort’ (C)  Found ‘exit’, possibly from ‘exit’ (C)  Found ‘printf’, possibly from ‘printf’ (C)  Found ‘putchar’, possibly from ‘putchar’ (C)  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)  Found ‘rand’, possibly from ‘rand’ (C)  Found ‘sprintf’, possibly from ‘sprintf’ (C)  Found ‘srand’, possibly from ‘srand’ (C)  Found ‘srand48’, possibly from ‘srand48’ (C)  Found ‘stderr’, possibly from ‘stderr’ (C)  Found ‘stdout’, possibly from ‘stdout’ (C)Compiled code should not call entry points which might terminate R norwrite to stdout/stderr instead of to the console, nor use Fortran I/Onor system RNGs nor [v]sprintf. The detected symbols are linked intothe code but might come from libraries and not actually be called.See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.* checking files in ‘vignettes’ ... OK* checking examples ... OK* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘runTests.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking running R code from vignettes ... SKIPPED* checking re-building of vignette outputs ... SKIPPED* checking PDF version of manual ... OK* DONEStatus: 2 WARNINGs, 2 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD INSTALL Rgraphviz###############################################################################################################################################################* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’* installing *source* package ‘Rgraphviz’ ...** this is package ‘Rgraphviz’ version ‘2.54.0’** using staged installationconfigure: Using bundled Graphviz.configure: Searching for the compilers specified by R.checking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17checking whether the C compiler works... yeschecking for C compiler default output file name... a.outchecking for suffix of executables... checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether the compiler supports GNU C... yeschecking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 accepts -g... yeschecking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 option to enable C11 features... none neededchecking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -Echecking whether the compiler supports GNU C++... yeschecking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ accepts -g... yeschecking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ option to enable C++11 features... none neededconfigure: Preparing to compile Graphviz.configure: Configuring bundled Graphviz.checking build system type... aarch64-unknown-linux-gnuchecking host system type... aarch64-unknown-linux-gnuchecking for a BSD-compatible install... /usr/bin/install -cchecking whether build environment is sane... yeschecking for a thread-safe mkdir -p... /usr/bin/mkdir -pchecking for gawk... gawkchecking whether make sets $(MAKE)... yeschecking whether make supports nested variables... yeschecking for style of include used by make... GNUchecking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17checking whether the C compiler works... yeschecking for C compiler default output file name... a.outchecking for suffix of executables... checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether we are using the GNU C compiler... yeschecking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 accepts -g... yeschecking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 option to accept ISO C89... none neededchecking dependency style of /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17... gcc3checking for library containing strerror... none requiredchecking for flex... flexchecking lex output file root... lex.yychecking lex library... none neededchecking whether yytext is a pointer... nochecking for bison... bison -ychecking for gawk... (cached) gawkchecking whether ln -s works... yeschecking for sed... /usr/bin/sedchecking for grep... grepchecking for sort... sortchecking for groff... groffchecking for ps2pdf... ps2pdfchecking for pstopdf... (cached) ps2pdfchecking for pkg-config... /usr/bin/pkg-configchecking pkg-config is at least version 0.9.0... yeschecking for tclsh8.6... /usr/bin/tclsh8.6checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 and cc understand -c and -o together... yeschecking whether we are using the GNU C++ compiler... yeschecking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ accepts -g... yeschecking dependency style of /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++... gcc3checking for gcc... gccchecking whether we are using the GNU Objective C compiler... nochecking whether gcc accepts -g... nochecking dependency style of gcc... gcc3checking for inline... inlinechecking for windres... nochecking for an ANSI C-conforming const... yeschecking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -Echecking for grep that handles long lines and -e... grepchecking for egrep... grep -Echecking for ANSI C header files... yeschecking for sys/types.h... yeschecking for sys/stat.h... yeschecking for stdlib.h... yeschecking for string.h... yeschecking for memory.h... yeschecking for strings.h... yeschecking for inttypes.h... yeschecking for stdint.h... yeschecking for unistd.h... yeschecking for mode_t... yeschecking for pid_t... yeschecking for size_t... yeschecking for ssize_t... yeschecking for uid_t in sys/types.h... yeschecking stdarg.h usability... yeschecking stdarg.h presence... yeschecking for stdarg.h... yeschecking stddef.h usability... yeschecking stddef.h presence... yeschecking for stddef.h... yeschecking for stddef.h... (cached) yeschecking for stdlib.h... (cached) yeschecking for stdint.h... (cached) yeschecking malloc.h usability... yeschecking malloc.h presence... yeschecking for malloc.h... yeschecking fcntl.h usability... yeschecking fcntl.h presence... yeschecking for fcntl.h... yeschecking search.h usability... yeschecking search.h presence... yeschecking for search.h... yeschecking getopt.h usability... yeschecking getopt.h presence... yeschecking for getopt.h... yeschecking pthread.h usability... yeschecking pthread.h presence... yeschecking for pthread.h... yeschecking values.h usability... yeschecking values.h presence... yeschecking for values.h... yeschecking float.h usability... yeschecking float.h presence... yeschecking for float.h... yeschecking limits.h usability... yeschecking limits.h presence... yeschecking for limits.h... yeschecking termios.h usability... yeschecking termios.h presence... yeschecking for termios.h... yeschecking errno.h usability... yeschecking errno.h presence... yeschecking for errno.h... yeschecking time.h usability... yeschecking time.h presence... yeschecking for time.h... yeschecking for unistd.h... (cached) yeschecking fenv.h usability... yeschecking fenv.h presence... yeschecking for fenv.h... yeschecking for string.h... (cached) yeschecking for strings.h... (cached) yeschecking for inttypes.h... (cached) yeschecking setjmp.h usability... yeschecking setjmp.h presence... yeschecking for setjmp.h... yeschecking sys/time.h usability... yeschecking sys/time.h presence... yeschecking for sys/time.h... yeschecking sys/times.h usability... yeschecking sys/times.h presence... yeschecking for sys/times.h... yeschecking for sys/types.h... (cached) yeschecking sys/select.h usability... yeschecking sys/select.h presence... yeschecking for sys/select.h... yeschecking fpu_control.h usability... yeschecking fpu_control.h presence... yeschecking for fpu_control.h... yeschecking sys/fpu.h usability... nochecking sys/fpu.h presence... nochecking for sys/fpu.h... nochecking sys/socket.h usability... yeschecking sys/socket.h presence... yeschecking for sys/socket.h... yeschecking for sys/stat.h... (cached) yeschecking sys/mman.h usability... yeschecking sys/mman.h presence... yeschecking for sys/mman.h... yeschecking sys/ioctl.h usability... yeschecking sys/ioctl.h presence... yeschecking for sys/ioctl.h... yeschecking sys/inotify.h usability... yeschecking sys/inotify.h presence... yeschecking for sys/inotify.h... yeschecking langinfo.h usability... yeschecking langinfo.h presence... yeschecking for langinfo.h... yeschecking libintl.h usability... yeschecking libintl.h presence... yeschecking for libintl.h... yeschecking crt_externs.h usability... nochecking crt_externs.h presence... nochecking for crt_externs.h... nochecking whether time.h and sys/time.h may both be included... yeschecking for dirent.h that defines DIR... yeschecking for library containing opendir... none requiredchecking for stdbool.h that conforms to C99... yeschecking for _Bool... yeschecking for socklen_t... yeschecking for bool... yeschecking for struct dioattr... nochecking for main in -lm... yeschecking for feenableexcept... yeschecking for fesetenv... yeschecking libgen.h usability... yeschecking libgen.h presence... yeschecking for libgen.h... yeschecking for basename in -lgen... nochecking for working alloca.h... yeschecking for alloca... yeschecking for lrand48... yeschecking for drand48... yeschecking for srand48... yeschecking for setmode... nochecking for setenv... yeschecking for getenv... yeschecking for __freadable... yeschecking for _sysconf... nochecking for getrusage... yeschecking for strerror... yeschecking for cbrt... nochecking for lsqrt... nochecking for vsnprintf... yeschecking for strtoul... yeschecking for strtoll... yeschecking for strtoull... yeschecking for uname... yeschecking for memset... yeschecking for nl_langinfo... yeschecking for pow... nochecking for sqrt... nochecking for strchr... yeschecking for strdup... yeschecking for strerror... (cached) yeschecking for strstr... yeschecking for _NSGetEnviron... nochecking for strcasecmp... yeschecking for strncasecmp... yeschecking for strcasestr... yeschecking for a sed that does not truncate output... /usr/bin/sedchecking for fgrep... grep -Fchecking for ld used by /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17... /usr/bin/ldchecking if the linker (/usr/bin/ld) is GNU ld... yeschecking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -Bchecking the name lister (/usr/bin/nm -B) interface... BSD nmchecking the maximum length of command line arguments... 1572864checking whether the shell understands some XSI constructs... yeschecking whether the shell understands "+="... yeschecking for /usr/bin/ld option to reload object files... -rchecking for objdump... objdumpchecking how to recognize dependent libraries... pass_allchecking for ar... archecking for strip... stripchecking for ranlib... ranlibchecking command to parse /usr/bin/nm -B output from /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 object... okchecking for dlfcn.h... yeschecking whether we are using the GNU C++ compiler... (cached) yeschecking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ accepts -g... (cached) yeschecking dependency style of /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++... (cached) gcc3checking how to run the C++ preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -Echecking for objdir... .libschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 supports -fno-rtti -fno-exceptions... nochecking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 option to produce PIC... -fPIC -DPICchecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 PIC flag -fPIC -DPIC works... yeschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 static flag -static works... yeschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 supports -c -o file.o... yeschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 supports -c -o file.o... (cached) yeschecking whether the /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 linker (/usr/bin/ld) supports shared libraries... yeschecking dynamic linker characteristics... GNU/Linux ld.sochecking how to hardcode library paths into programs... immediatechecking for shl_load... nochecking for shl_load in -ldld... nochecking for dlopen... yeschecking whether a program can dlopen itself... yeschecking whether a statically linked program can dlopen itself... nochecking whether stripping libraries is possible... yeschecking if libtool supports shared libraries... yeschecking whether to build shared libraries... nochecking whether to build static libraries... yeschecking for ld used by /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++... /usr/bin/ldchecking if the linker (/usr/bin/ld) is GNU ld... yeschecking whether the /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ linker (/usr/bin/ld) supports shared libraries... yeschecking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ option to produce PIC... -fPIC -DPICchecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ PIC flag -fPIC -DPIC works... yeschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ static flag -static works... nochecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ supports -c -o file.o... yeschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ supports -c -o file.o... (cached) yeschecking whether the /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ linker (/usr/bin/ld) supports shared libraries... yeschecking dynamic linker characteristics... GNU/Linux ld.sochecking how to hardcode library paths into programs... immediatechecking which extension is used for runtime loadable modules... .sochecking which variable specifies run-time module search path... LD_LIBRARY_PATHchecking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib64/NetworkManager/1.44.2-3.oe2403 /usr/lib64/acl /usr/lib64 /usr/lib64/graphviz /usr/lib64 /usr/lib64/libproxy /usr/lib64 /usr/lib64/man-db /usr/lib64/mysql /usr/lib64/openmpi/lib /usr/lib64/pulseaudio/modules /usr/lib64/pulseaudio/ /usr/libexec/sudo /usr/lib64/systemd /usr/lib64/tracker-3.0 /usr/lib64/vala-0.56 /usr/lib64/perl5/CORE checking for library containing dlopen... none requiredchecking for dlerror... yeschecking for shl_load... (cached) nochecking for shl_load in -ldld... (cached) nochecking for dld_link in -ldld... nochecking for _ prefix in compiled symbols... nochecking whether deplibs are loaded by dlopen... yeschecking for argz.h... yeschecking for error_t... yeschecking for argz_add... yeschecking for argz_append... yeschecking for argz_count... yeschecking for argz_create_sep... yeschecking for argz_insert... yeschecking for argz_next... yeschecking for argz_stringify... yeschecking if argz actually works... yeschecking whether libtool supports -dlopen/-dlpreopen... yeschecking for ltdl.h... nochecking where to find libltdl headers... -I${top_srcdir}/libltdlchecking where to find libltdl library... ${top_build_prefix}libltdl/libltdlc.lachecking for unistd.h... (cached) yeschecking for dl.h... nochecking for sys/dl.h... nochecking for dld.h... nochecking for mach-o/dyld.h... nochecking for dirent.h... yeschecking for closedir... yeschecking for opendir... yeschecking for readdir... yeschecking for strlcat... yeschecking for strlcpy... yeschecking for X... disabledconfigure: WARNING: X11 not available.checking tcl.h usability... yeschecking tcl.h presence... yeschecking for tcl.h... yesconfigure: WARNING: Unable to find tclConfig.sh. The Tcl packages will not be builtconfigure: WARNING: No Tcl. The Tk packages will not be built eitherchecking for connect... yeschecking for gethostbyname... yeschecking for main in -lXpm... noconfigure: WARNING: Optional Xpm library not availablechecking X11/Intrinsic.h usability... yeschecking X11/Intrinsic.h presence... yeschecking for X11/Intrinsic.h... yeschecking for X11/Xaw/Text.h... noconfigure: WARNING: Optional Xaw library not available - missing headerschecking zlib.h usability... yeschecking zlib.h presence... yeschecking for zlib.h... yeschecking for main in -lz... yeschecking for deflateBound... yeschecking for GDK_PIXBUF... yeschecking for GTK... yeschecking for GTKGL... nochecking for GTKGLEXT... nochecking for GLADE... nochecking for qmake-qt4... nochecking for qmake-qt3... nochecking for qmake... nochecking for sincos... yeschecking if FILE struct contains _cnt... nochecking if FILE struct contains _r... nochecking if FILE struct contains _next... nochecking if FILE struct contains _IO_read_end... nochecking if errno externs are declared... nochecking if getopt externs are declared... yeschecking if intptr_t is declared... yeschecking if assert needs __eprintf... nochecking that generated files are newer than configure... doneconfigure: creating ./config.statusconfig.status: creating Makefileconfig.status: creating lib/Makefileconfig.status: creating lib/cdt/Makefileconfig.status: creating lib/cdt/libcdt.pcconfig.status: creating lib/graph/Makefileconfig.status: creating lib/graph/libgraph.pcconfig.status: creating lib/rbtree/Makefileconfig.status: creating lib/pathplan/Makefileconfig.status: creating lib/pathplan/libpathplan.pcconfig.status: creating lib/dotgen/Makefileconfig.status: creating lib/neatogen/Makefileconfig.status: creating lib/fdpgen/Makefileconfig.status: creating lib/sparse/Makefileconfig.status: creating lib/sfdpgen/Makefileconfig.status: creating lib/osage/Makefileconfig.status: creating lib/circogen/Makefileconfig.status: creating lib/twopigen/Makefileconfig.status: creating lib/patchwork/Makefileconfig.status: creating lib/pack/Makefileconfig.status: creating lib/ortho/Makefileconfig.status: creating lib/common/Makefileconfig.status: creating lib/vpsc/Makefileconfig.status: creating lib/gvc/Makefileconfig.status: creating lib/gvc/libgvc.pcconfig.status: creating lib/xdot/Makefileconfig.status: creating lib/xdot/libxdot.pcconfig.status: creating plugin/Makefileconfig.status: creating plugin/core/Makefileconfig.status: creating plugin/dot_layout/Makefileconfig.status: creating plugin/neato_layout/Makefileconfig.status: creating graphviz.specconfig.status: creating Doxyfileconfig.status: creating config.hconfig.status: executing depfiles commandsconfig.status: executing libtool commands=== configuring in libltdl (/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/libltdl)configure: running /bin/sh ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix'  'CC=/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17' 'CXX=/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2 -Wall -Werror=format-security' 'LDFLAGS=-L/usr/local/lib' '--libdir=/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib' '--includedir=/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'CPPFLAGS=-I/usr/local/include' 'R_LIBS=/home/biocbuild/R/R-4.5.0/site-library/00LOCK-Rgraphviz/00new:/home/biocbuild/R/R/site-library' '--enable-ltdl-convenience' --cache-file=/dev/null --srcdir=.checking for a BSD-compatible install... /usr/bin/install -cchecking whether build environment is sane... yeschecking for a thread-safe mkdir -p... /usr/bin/mkdir -pchecking for gawk... gawkchecking whether make sets $(MAKE)... yeschecking build system type... aarch64-unknown-linux-gnuchecking host system type... aarch64-unknown-linux-gnuchecking for style of include used by make... GNUchecking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17checking whether the C compiler works... yeschecking for C compiler default output file name... a.outchecking for suffix of executables... checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether we are using the GNU C compiler... yeschecking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 accepts -g... yeschecking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 option to accept ISO C89... none neededchecking dependency style of /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17... gcc3checking for a sed that does not truncate output... /usr/bin/sedchecking for grep that handles long lines and -e... /usr/bin/grepchecking for egrep... /usr/bin/grep -Echecking for fgrep... /usr/bin/grep -Fchecking for ld used by /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17... /usr/bin/ldchecking if the linker (/usr/bin/ld) is GNU ld... yeschecking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -Bchecking the name lister (/usr/bin/nm -B) interface... BSD nmchecking whether ln -s works... yeschecking the maximum length of command line arguments... 1572864checking whether the shell understands some XSI constructs... yeschecking whether the shell understands "+="... yeschecking for /usr/bin/ld option to reload object files... -rchecking for objdump... objdumpchecking how to recognize dependent libraries... pass_allchecking for ar... archecking for strip... stripchecking for ranlib... ranlibchecking command to parse /usr/bin/nm -B output from /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 object... okchecking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -Echecking for ANSI C header files... yeschecking for sys/types.h... yeschecking for sys/stat.h... yeschecking for stdlib.h... yeschecking for string.h... yeschecking for memory.h... yeschecking for strings.h... yeschecking for inttypes.h... yeschecking for stdint.h... yeschecking for unistd.h... yeschecking for dlfcn.h... yeschecking for objdir... .libschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 supports -fno-rtti -fno-exceptions... nochecking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 option to produce PIC... -fPIC -DPICchecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 PIC flag -fPIC -DPIC works... yeschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 static flag -static works... yeschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 supports -c -o file.o... yeschecking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 supports -c -o file.o... (cached) yeschecking whether the /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 linker (/usr/bin/ld) supports shared libraries... yeschecking dynamic linker characteristics... GNU/Linux ld.sochecking how to hardcode library paths into programs... immediatechecking for shl_load... nochecking for shl_load in -ldld... nochecking for dlopen... yeschecking whether a program can dlopen itself... yeschecking whether a statically linked program can dlopen itself... nochecking whether stripping libraries is possible... yeschecking if libtool supports shared libraries... yeschecking whether to build shared libraries... nochecking whether to build static libraries... yeschecking which extension is used for runtime loadable modules... .sochecking which variable specifies run-time module search path... LD_LIBRARY_PATHchecking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib64/NetworkManager/1.44.2-3.oe2403 /usr/lib64/acl /usr/lib64 /usr/lib64/graphviz /usr/lib64 /usr/lib64/libproxy /usr/lib64 /usr/lib64/man-db /usr/lib64/mysql /usr/lib64/openmpi/lib /usr/lib64/pulseaudio/modules /usr/lib64/pulseaudio/ /usr/libexec/sudo /usr/lib64/systemd /usr/lib64/tracker-3.0 /usr/lib64/vala-0.56 /usr/lib64/perl5/CORE checking for library containing dlopen... none requiredchecking for dlerror... yeschecking for shl_load... (cached) nochecking for shl_load in -ldld... (cached) nochecking for dld_link in -ldld... nochecking for _ prefix in compiled symbols... nochecking whether deplibs are loaded by dlopen... yeschecking for argz.h... yeschecking for error_t... yeschecking for argz_add... yeschecking for argz_append... yeschecking for argz_count... yeschecking for argz_create_sep... yeschecking for argz_insert... yeschecking for argz_next... yeschecking for argz_stringify... yeschecking if argz actually works... yeschecking whether libtool supports -dlopen/-dlpreopen... yeschecking for unistd.h... (cached) yeschecking for dl.h... nochecking for sys/dl.h... nochecking for dld.h... nochecking for mach-o/dyld.h... nochecking for dirent.h... yeschecking for closedir... yeschecking for opendir... yeschecking for readdir... yeschecking for strlcat... yeschecking for strlcpy... yeschecking that generated files are newer than configure... doneconfigure: creating ./config.statusconfig.status: creating Makefileconfig.status: creating config.hconfig.status: executing depfiles commandsconfig.status: executing libtool commands----------------------------------------------------------------graphviz-2.28.0 will be compiled with the following:options:  cgraph:        No (disabled by default - experimental)  digcola:       Yes  expat:         No (disabled)  fontconfig:    No (disabled)  freetype:      No (disabled)  glut:          No (disabled)  gts:           No (disabled)  ipsepcola:     No (disabled by default - C++ portability issues)  ltdl:          No (disabled)  ortho:         Yes  png:           No (disabled)  jpeg:          No (disabled)  sfdp:          Yes  shared:        No (disabled)  static:        Yes  qt:            No (qmake not found)commands:  dot:           Yes (always enabled)  neato:         Yes (always enabled)  fdp:           Yes (always enabled)  circo:         Yes (always enabled)  twopi:         Yes (always enabled)  gvpr:          Yes (always enabled)  gvmap:         Yes (always enabled)  lefty:         No (missing Xaw headers)  smyrna:        No (disabled by default - experimental)  gvedit:        No (qmake not found)plugin libraries:  dot_layout:    Yes (always enabled)  neato_layout:  Yes (always enabled)  core:          Yes (always enabled)  devil:         No (disabled)  gd:            No (disabled)  gdiplus:       No (disabled by default - Windows only)  gdk_pixbuf:    Yes  ghostscript:   No (disabled)  glitz:         No (disabled by default - incomplete)  gtk:           Yes  lasi:          No (disabled)  ming:          No (disabled by default - incomplete)  pangocairo:    No (disabled)  quartz:        No (disabled by default - Mac only)  rsvg:          No (disabled)  visio:         No (disabled by default - experimental)  xlib:          No (disabled or unavailable)language extensions:  gv_sharp:      No (swig not available)  gv_go:         No (disabled by default - experimental)  gv_guile:      No (swig not available)  gv_io:         No (disabled by default - no swig support yet)  gv_java:       No (swig not available)  gv_lua:        No (swig not available)  gv_ocaml:      No (swig not available)  gv_perl:       No (swig not available)  gv_php:        No (swig not available)  gv_python:     No (swig not available)  gv_python23:   No (disabled by default - for multiversion installs)  gv_python24:   No (disabled by default - for multiversion installs)  gv_python25:   No (disabled by default - for multiversion installs)  gv_python26:   No (disabled by default - for multiversion installs)  gv_python27:   No (disabled by default - for multiversion installs)  gv_R:          No (swig not available)  gv_ruby:       No (swig not available)  gv_tcl:        No (tcl not available)  tcldot:        No (tcl not available)  tclpathplan:   No (tcl not available)  gdtclft:       No (tcl not available)  tkspline:      No (tk not available)grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.hmake  install-recursivemake[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz'Making install in libltdlmake[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/libltdl'make  install-ammake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/libltdl'/bin/sh ./libtool  --tag=CC   --mode=compile /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include  -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.clibtool: compile:  /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c  -fPIC -DPIC -o dlopen.omv -f .deps/dlopen.Tpo .deps/dlopen.Plo/bin/sh ./libtool --tag=CC   --mode=link /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17  -g -O2 -module -avoid-version -L/usr/local/lib -o dlopen.la  dlopen.lo  libtool: link: ar cru .libs/dlopen.a  dlopen.olibtool: link: ranlib .libs/dlopen.alibtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" )/bin/sh ./libtool  --tag=CC   --mode=compile /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include  -g -O2 -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c -o libltdlc_la-preopen.lo `test -f 'loaders/preopen.c' || echo './'`loaders/preopen.clibtool: compile:  /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c  -fPIC -DPIC -o libltdlc_la-preopen.omv -f .deps/libltdlc_la-preopen.Tpo .deps/libltdlc_la-preopen.Plo/bin/sh ./libtool  --tag=CC   --mode=compile /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include  -g -O2 -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c -o libltdlc_la-lt__alloc.lo `test -f 'lt__alloc.c' || echo './'`lt__alloc.clibtool: compile:  /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c  -fPIC -DPIC -o libltdlc_la-lt__alloc.omv -f .deps/libltdlc_la-lt__alloc.Tpo .deps/libltdlc_la-lt__alloc.Plo/bin/sh ./libtool  --tag=CC   --mode=compile /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include  -g -O2 -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c -o libltdlc_la-lt_dlloader.lo `test -f 'lt_dlloader.c' || echo './'`lt_dlloader.clibtool: compile:  /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c  -fPIC -DPIC -o libltdlc_la-lt_dlloader.omv -f .deps/libltdlc_la-lt_dlloader.Tpo .deps/libltdlc_la-lt_dlloader.Plo/bin/sh ./libtool  --tag=CC   --mode=compile /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include  -g -O2 -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c -o libltdlc_la-lt_error.lo `test -f 'lt_error.c' || echo './'`lt_error.clibtool: compile:  /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c  -fPIC -DPIC -o libltdlc_la-lt_error.omv -f .deps/libltdlc_la-lt_error.Tpo .deps/libltdlc_la-lt_error.Plo/bin/sh ./libtool  --tag=CC   --mode=compile /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include  -g -O2 -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c -o libltdlc_la-ltdl.lo `test -f 'ltdl.c' || echo './'`ltdl.clibtool: compile:  /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c  -fPIC -DPIC -o libltdlc_la-ltdl.omv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo/bin/sh ./libtool  --tag=CC   --mode=compile /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include  -g -O2 -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c -o libltdlc_la-slist.lo `test -f 'slist.c' || echo './'`slist.clibtool: compile:  /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c  -fPIC -DPIC -o libltdlc_la-slist.omv -f .deps/libltdlc_la-slist.Tpo .deps/libltdlc_la-slist.Plo/bin/sh ./libtool --tag=CC   --mode=link /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17  -g -O2 -no-undefined -dlpreopen dlopen.la  -L/usr/local/lib -o libltdlc.la  libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo  libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmTlibtool: link: (cd .libs && /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -g -O2 -c -fno-builtin  -fPIC -DPIC "libltdlcS.c")libtool: link: rm -f ".libs/libltdlcS.c" ".libs/libltdlc.nm" ".libs/libltdlc.nmS" ".libs/libltdlc.nmT"libtool: link: (cd .libs/libltdlc.lax/dlopen.a && ar x "/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a")libtool: link: ar cru .libs/libltdlc.a  libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o .libs/libltdlcS.o  .libs/libltdlc.lax/dlopen.a/dlopen.o libtool: link: ranlib .libs/libltdlc.alibtool: link: rm -fr .libs/libltdlc.laxlibtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )make[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/libltdl'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/libltdl'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/libltdl'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/libltdl'Making install in libmake[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib'Making install in cdtmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'  CC       dtclose.lo  CC       dtdisc.lodtdisc.c:13:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]   13 | static Void_t* dtmemory(dt, addr, size, disc)      |                ^~~~~~~~  CC       dtextract.lo  CC       dtflatten.lo  CC       dthash.lodthash.c:15:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]   15 | static void dthtab(dt)      |             ^~~~~~dthash.c:81:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]   81 | static Void_t* dthash(dt,obj,type)      |                ^~~~~~dthash.c: In function 'dthash':dthash.c:306:34: warning: 'r' may be used uninitialized [-Wmaybe-uninitialized]  306 |                                 (*dt->memoryf)(dt,(Void_t*)r,0,disc);      |                                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dthash.c:87:30: note: 'r' was declared here   87 |         reg Dtlink_t    *t, *r, *p;      |                              ^  CC       dtlist.lodtlist.c:11:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]   11 | static Void_t* dtlist(dt, obj, type)      |                ^~~~~~  CC       dtmethod.lo  CC       dtopen.lo  CC       dtrenew.lo  CC       dtrestore.lo  CC       dtsize.lodtsize.c:11:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]   11 | static int treecount(e)      |            ^~~~~~~~~  CC       dtstat.lodtstat.c:11:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]   11 | static void dttstat(ds,root,depth,level)      |             ^~~~~~~dtstat.c:31:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]   31 | static void dthstat(data, ds, count)      |             ^~~~~~~  CC       dtstrhash.lo  CC       dttree.lodttree.c:14:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]   14 | static Void_t* dttree(dt,obj,type)      |                ^~~~~~dttree.c: In function 'dttree':dttree.c:294:43: warning: 'me' may be used uninitialized [-Wmaybe-uninitialized]  294 |                                 me->right = link.left;dttree.c:23:34: note: 'me' was declared here   23 |         Dtlink_t        *l, *r, *me, link;      |                                  ^~  CC       dttreeset.lodttreeset.c:11:18: warning: function declaration isn't a prototype [-Wstrict-prototypes]   11 | static Dtlink_t* treebalance(list, size)      |                  ^~~~~~~~~~~  CC       dtview.lodtview.c:12:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]   12 | static Void_t* dtvsearch(dt,obj,type)      |                ^~~~~~~~~dtview.c: In function 'dtvsearch':dtview.c:20:30: warning: variable 'lk' set but not used [-Wunused-but-set-variable]   20 |         int             cmp, lk, sz, ky;      |                              ^~  CC       dtwalk.lodtwalk.c: In function 'dtwalk':dtwalk.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]   14 | int(*           userf)();      | ^~~  CCLD     libcdt.la  CCLD     libcdt_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/cdt' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libcdt.la '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib'libtool: install: /usr/bin/install -c .libs/libcdt.lai /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.lalibtool: install: /usr/bin/install -c .libs/libcdt.a /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.alibtool: finish: PATH="/home/biocbuild/.pixi/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/share/Modules/bin:/usr/local/ensembl-vep:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/bioconductor/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/bioconductor/openbabel-3.1.1/bin:/opt/meme/bin:/home/biocbuild/dotnet:/opt/meme/libexec/meme-5.5.5:/home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin:/home/biocbuild/bioconductor/quarto-1.7.32/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib----------------------------------------------------------------------Libraries have been installed in:   /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/libIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify the full pathname of the library, or use the `-LLIBDIR'flag during linking and do at least one of the following:   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable     during execution   - add LIBDIR to the `LD_RUN_PATH' environment variable     during linking   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag   - have your system administrator add LIBDIR to `/etc/ld.so.conf'See any operating system documentation about shared libraries formore information, such as the ld(1) and ld.so(8) manual pages.---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 cdt.3 '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 cdt.3.pdf '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libcdt.pc '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 cdt.h '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'Making install in graphmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/graph'  CC       attribs.lo  CC       agxbuf.lo  CC       edge.lo  CC       graph.lograph.c: In function 'agclose':graph.c:374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]  374 |     if (g->attr)      |     ^~graph.c:376:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'  376 |         if (g->didset)      |         ^~  CC       graphio.lo  CC       lexer.lolexer.c: In function 'scan_token':lexer.c:141:11: warning: comparison between pointer and zero character constant [-Wpointer-compare]  141 |     if (p == '\0')      |           ^~lexer.c:141:9: note: did you mean to dereference the pointer?  141 |     if (p == '\0')      |         ^lexer.c:147:12: warning: pointer targets in returning 'unsigned char *' from a function with return type 'char *' differ in signedness [-Wpointer-sign]  147 |     return p;      |            ^lexer.c: In function 'html_pair':lexer.c:322:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]  322 |     int rc, depth = 1;      |         ^~In file included from lexer.c:20:lexer.c: In function 'aglex':agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~lexer.c:413:36: note: in expansion of macro 'agxbuse'  413 |         aglval.str = agstrdup_html(agxbuse(&xb));      |                                    ^~~~~~~lexer.c:435:33: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign]  435 |             LexPtr = scan_token(LexPtr, tbuf);      |                                 ^~~~~~      |                                 |      |                                 char *lexer.c:136:40: note: expected 'unsigned char *' but argument is of type 'char *'  136 | static char *scan_token(unsigned char *p, unsigned char *token)      |                         ~~~~~~~~~~~~~~~^lexer.c:435:41: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign]  435 |             LexPtr = scan_token(LexPtr, tbuf);      |                                         ^~~~      |                                         |      |                                         char *lexer.c:136:58: note: expected 'unsigned char *' but argument is of type 'char *'  136 | static char *scan_token(unsigned char *p, unsigned char *token)      |                                           ~~~~~~~~~~~~~~~^~~~~  CC       node.lo  CC       parser.lo  CC       refstr.lo  CC       trie.lo  CCLD     libgraph.la  CCLD     libgraph_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/graph' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgraph.la '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib'libtool: install: /usr/bin/install -c .libs/libgraph.lai /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.lalibtool: install: /usr/bin/install -c .libs/libgraph.a /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.alibtool: finish: PATH="/home/biocbuild/.pixi/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/share/Modules/bin:/usr/local/ensembl-vep:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/bioconductor/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/bioconductor/openbabel-3.1.1/bin:/opt/meme/bin:/home/biocbuild/dotnet:/opt/meme/libexec/meme-5.5.5:/home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin:/home/biocbuild/bioconductor/quarto-1.7.32/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib----------------------------------------------------------------------Libraries have been installed in:   /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/libIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify the full pathname of the library, or use the `-LLIBDIR'flag during linking and do at least one of the following:   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable     during execution   - add LIBDIR to the `LD_RUN_PATH' environment variable     during linking   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag   - have your system administrator add LIBDIR to `/etc/ld.so.conf'See any operating system documentation about shared libraries formore information, such as the ld(1) and ld.so(8) manual pages.---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 graph.3 '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 graph.3.pdf '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libgraph.pc '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 graph.h '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/graph'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/graph'Making install in pathplanmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'  CC       cvt.locvt.c:276:13: warning: 'append_bezier' defined but not used [-Wunused-function]  276 | static void append_bezier(Ppoint_t * bezier)      |             ^~~~~~~~~~~~~  CC       inpoly.lo  CC       route.loroute.c:107:29: warning: argument 4 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=]  107 |                  Ppoint_t * evs, Ppolyline_t * output)      |                  ~~~~~~~~~~~^~~In file included from pathutil.h:20,                 from route.c:21:pathplan.h:37:39: note: previously declared as an array 'Pvector_t[2]' {aka 'struct Pxy_t[2]'}   37 |                             Pvector_t endpoint_slopes[2],      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~~  CC       shortest.loshortest.c:103:47: warning: argument 2 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=]  103 | int Pshortestpath(Ppoly_t * polyp, Ppoint_t * eps, Ppolyline_t * output)      |                                    ~~~~~~~~~~~^~~In file included from pathutil.h:20,                 from shortest.c:22:pathplan.h:31:59: note: previously declared as an array 'Ppoint_t[2]' {aka 'struct Pxy_t[2]'}   31 |     extern int Pshortestpath(Ppoly_t * boundary, Ppoint_t endpoints[2],      |                                                  ~~~~~~~~~^~~~~~~~~~~~  CC       shortestpth.lo  CC       solvers.lo  CC       triang.lo  CC       util.lo  CC       visibility.lo  CCLD     libpathplan.la  CCLD     libpathplan_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libpathplan.la '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib'libtool: install: /usr/bin/install -c .libs/libpathplan.lai /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.lalibtool: install: /usr/bin/install -c .libs/libpathplan.a /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.alibtool: finish: PATH="/home/biocbuild/.pixi/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/share/Modules/bin:/usr/local/ensembl-vep:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/bioconductor/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/bioconductor/openbabel-3.1.1/bin:/opt/meme/bin:/home/biocbuild/dotnet:/opt/meme/libexec/meme-5.5.5:/home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin:/home/biocbuild/bioconductor/quarto-1.7.32/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib----------------------------------------------------------------------Libraries have been installed in:   /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/libIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify the full pathname of the library, or use the `-LLIBDIR'flag during linking and do at least one of the following:   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable     during execution   - add LIBDIR to the `LD_RUN_PATH' environment variable     during linking   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag   - have your system administrator add LIBDIR to `/etc/ld.so.conf'See any operating system documentation about shared libraries formore information, such as the ld(1) and ld.so(8) manual pages.---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 pathplan.3 '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 pathplan.3.pdf '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libpathplan.pc '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'Making install in vpscmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'make[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'Making install in rbtreemake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'  CC       misc.lo  CC       red_black_tree.lo  CC       stack.lo  CCLD     librbtree_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'Making install in orthomake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'  CC       fPQ.lo  CC       intset.lo  CC       maze.lomaze.c: In function 'mkMazeGraph':maze.c:325:20: warning: variable 'ncnt' set but not used [-Wunused-but-set-variable]  325 |     int nsides, i, ncnt, maxdeg;      |                    ^~~~  CC       ortho.loortho.c: In function 'addLoop':ortho.c:461:16: warning: variable 'wt' set but not used [-Wunused-but-set-variable]  461 |         double wt;      |                ^~ortho.c: In function 'addNodeEdges':ortho.c:497:16: warning: variable 'wt' set but not used [-Wunused-but-set-variable]  497 |         double wt;      |                ^~ortho.c: In function 'putSeg':ortho.c:545:5: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]  545 |     fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->p.p1,seg->comm_coord,      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  546 |       seg->p.p2, seg->comm_coord, bendToStr (seg->l1), bendToStr (seg->l2));      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ortho.c:518:9: note: 's' was declared here  518 |   char* s;      |         ^ortho.c:545:5: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]  545 |     fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->p.p1,seg->comm_coord,      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  546 |       seg->p.p2, seg->comm_coord, bendToStr (seg->l1), bendToStr (seg->l2));      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ortho.c:518:9: note: 's' was declared here  518 |   char* s;      |         ^ortho.c:542:5: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]  542 |     fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->comm_coord, seg->p.p1,      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  543 |       seg->comm_coord, seg->p.p2, bendToStr (seg->l1), bendToStr (seg->l2));      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ortho.c:518:9: note: 's' was declared here  518 |   char* s;      |         ^ortho.c:542:5: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]  542 |     fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->comm_coord, seg->p.p1,      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  543 |       seg->comm_coord, seg->p.p2, bendToStr (seg->l1), bendToStr (seg->l2));      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ortho.c:518:9: note: 's' was declared here  518 |   char* s;      |         ^ortho.c: In function 'orthoEdges':ortho.c:1303:25: warning: 'ps' may be used uninitialized [-Wmaybe-uninitialized] 1303 |                     if (isInPS (ps,hi,ti)) continue;      |                         ^~~~~~~~~~~~~~~~~ortho.c:1250:15: note: 'ps' was declared here 1250 |     PointSet* ps;      |               ^~In function 'convertSPtoRoute',    inlined from 'orthoEdges' at ortho.c:1341:25:ortho.c:179:25: warning: 'prevbp.y' may be used uninitialized [-Wmaybe-uninitialized]  179 |                 else if (prevbp.y > bp1.y) l1 = B_UP;      |                         ^ortho.c: In function 'orthoEdges':ortho.c:152:22: note: 'prevbp.y' was declared here  152 |     pointf bp1, bp2, prevbp;  /* bend points */      |                      ^~~~~~In function 'convertSPtoRoute',    inlined from 'orthoEdges' at ortho.c:1341:25:ortho.c:192:25: warning: 'prevbp.x' may be used uninitialized [-Wmaybe-uninitialized]  192 |                 else if (prevbp.x > bp1.x) l1 = B_RIGHT;      |                         ^ortho.c: In function 'orthoEdges':ortho.c:152:22: note: 'prevbp.x' was declared here  152 |     pointf bp1, bp2, prevbp;  /* bend points */      |                      ^~~~~~  CC       partition.lopartition.c: In function 'traverse_polygon':partition.c:328:7: warning: variable 'do_switch' set but not used [-Wunused-but-set-variable]  328 |   int do_switch = FALSE;      |       ^~~~~~~~~partition.c:327:7: warning: variable 'retval' set but not used [-Wunused-but-set-variable]  327 |   int retval;      |       ^~~~~~partition.c: In function 'partition':partition.c:731:9: warning: variable 'nt' set but not used [-Wunused-but-set-variable]  731 |     int nt;      |         ^~partition.c: In function 'make_new_monotone_poly':partition.c:212:7: warning: 'tp' may be used uninitialized [-Wmaybe-uninitialized]  212 |   int tp, tq;      |       ^~partition.c:274:5: warning: 'tq' may be used uninitialized [-Wmaybe-uninitialized]  274 |   q = vp1->vpos[iq];      |   ~~^~~~~~~~~~~~~~~partition.c:212:11: note: 'tq' was declared here  212 |   int tp, tq;      |           ^~partition.c: In function 'monotonate_trapezoids':partition.c:665:10: warning: 'size' may be used uninitialized [-Wmaybe-uninitialized]  665 |   return size;      |          ^~~~partition.c:620:12: note: 'size' was declared here  620 |     int i, size;      |            ^~~~  CC       rawgraph.lo  CC       sgraph.lo  CC       trapezoid.lotrapezoid.c:22:9: warning: "__USE_ISOC99" redefined   22 | #define __USE_ISOC99      |         ^~~~~~~~~~~~In file included from /usr/include/bits/libc-header-start.h:33,                 from /usr/include/string.h:26,                 from trapezoid.c:19:/usr/include/features.h:347:10: note: this is the location of the previous definition  347 | # define __USE_ISOC99           1      |          ^~~~~~~~~~~~trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]   66 | static int newnode()      |            ^~~~~~~trapezoid.c: In function 'add_segment':trapezoid.c:437:7: warning: variable 'tritop' set but not used [-Wunused-but-set-variable]  437 |   int tritop = 0, tribot = 0, is_swapped;      |       ^~~~~~trapezoid.c: In function 'add_segment.isra':trapezoid.c:996:3: warning: 'tfirstr' may be used uninitialized [-Wmaybe-uninitialized]  996 |   merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs);      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~trapezoid.c:434:7: note: 'tfirstr' was declared here  434 |   int tfirstr, tlastr, tfirstl, tlastl;      |       ^~~~~~~trapezoid.c:996:3: warning: 'tlastr' may be used uninitialized [-Wmaybe-uninitialized]  996 |   merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs);      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~trapezoid.c:434:16: note: 'tlastr' was declared here  434 |   int tfirstr, tlastr, tfirstl, tlastl;      |                ^~~~~~  CCLD     libortho_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'Making install in sparsemake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'  CC       SparseMatrix.loSparseMatrix.c: In function 'SparseMatrix_import_binary':SparseMatrix.c:629:48: warning: variable 'iread' set but not used [-Wunused-but-set-variable]  629 |   int m, n, nz, nzmax, type, format, property, iread;      |                                                ^~~~~  CC       general.lo  CC       BinaryHeap.loIn file included from general.h:21,                 from BinaryHeap.h:17,                 from BinaryHeap.c:14:BinaryHeap.c: In function 'BinaryHeap_sanity_check':BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses]  269 |   for (i = 0; i < h->len + IntStack_get_length(h->id_stack); i++) assert(mask[i] =- 1);      |                                                                          ^~~~  CC       IntStack.lo  CCLD     libsparse_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'Making install in patchworkmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'  CC       patchwork.loIn function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  231 |         cp = cp->rightsib;      |         ~~~^~~~~~~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:233:5: note: call to 'free' here  233 |     free (tp);      |     ^~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  231 |         cp = cp->rightsib;      |         ~~~^~~~~~~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:233:5: note: call to 'free' here  233 |     free (tp);      |     ^~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  231 |         cp = cp->rightsib;      |         ~~~^~~~~~~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:233:5: note: call to 'free' here  233 |     free (tp);      |     ^~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  231 |         cp = cp->rightsib;      |         ~~~^~~~~~~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:233:5: note: call to 'free' here  233 |     free (tp);      |     ^~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  231 |         cp = cp->rightsib;      |         ~~~^~~~~~~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:233:5: note: call to 'free' here  233 |     free (tp);      |     ^~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  231 |         cp = cp->rightsib;      |         ~~~^~~~~~~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:233:5: note: call to 'free' here  233 |     free (tp);      |     ^~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  231 |         cp = cp->rightsib;      |         ~~~^~~~~~~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2,    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:233:5: note: call to 'free' here  233 |     free (tp);      |     ^~~~~~~~~patchwork.c: In function 'freeTree':patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]  231 |         cp = cp->rightsib;      |         ~~~^~~~~~~~~~~~~~In function 'freeTree',    inlined from 'freeTree' at patchwork.c:230:2:patchwork.c:233:5: note: call to 'free' here  233 |     free (tp);      |     ^~~~~~~~~  CC       patchworkinit.lo  CC       tree_map.lo  CCLD     libpatchwork_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'Making install in commonmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/common'  CC       arrows.loarrows.c: In function 'arrowOrthoClip':arrows.c:397:28: warning: 'hlen' may be used uninitialized [-Wmaybe-uninitialized]  397 |             else r.y = p.y - hlen;      |                        ~~~~^~~~~~arrows.c:317:21: note: 'hlen' was declared here  317 |     double d, tlen, hlen, maxd;      |                     ^~~~  CC       colxlate.lo  CC       fontmetrics.lo  CC       args.lo  CC       memory.lo  CC       globals.lo  CC       htmllex.loIn file included from render.h:47,                 from htmllex.c:15:htmllex.c: In function 'error_context':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~htmllex.c:57:35: note: in expansion of macro 'agxbuse'   57 |     agerr(AGPREV, "... %s ...\n", agxbuse(state.xb));      |                                   ^~~~~~~  CC       htmlparse.loIn file included from render.h:47,                 from ../../lib/common/htmlparse.y:16:../../lib/common/htmlparse.y: In function 'appendFItemList':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~../../lib/common/htmlparse.y:193:25: note: in expansion of macro 'agxbuse'  193 |     fi->ti.str = strdup(agxbuse(ag));      |                         ^~~~~~~../../lib/common/htmlparse.y: In function 'htmlparse':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~../../lib/common/htmlparse.y:500:24: note: in expansion of macro 'agxbuse'  500 |           if (nonSpace(agxbuse(HTMLstate.str))) {      |                        ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~../../lib/common/htmlparse.y:511:24: note: in expansion of macro 'agxbuse'  511 |           if (nonSpace(agxbuse(HTMLstate.str))) {      |                        ^~~~~~~  CC       htmltable.loIn file included from render.h:47,                 from htmltable.c:35:htmltable.c: In function 'initAnchor':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~htmltable.c:299:14: note: in expansion of macro 'agxbuse'  299 |         id = agxbuse (&xb);      |              ^~~~~~~htmltable.c: In function 'nameOf':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~htmltable.c:1665:12: note: in expansion of macro 'agxbuse' 1665 |     return agxbuse(xb);      |            ^~~~~~~htmltable.c: In function 'make_html_label':htmltable.c:1828:12: warning: 'env.g' may be used uninitialized [-Wmaybe-uninitialized] 1828 |     g = env.g->root;      |         ~~~^~htmltable.c:1809:15: note: 'env' declared here 1809 |     htmlenv_t env;      |               ^~~  CC       input.loinput.c: In function 'dotneato_basename':input.c:136:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation]  136 |     while (*s) s++; s--;      |     ^~~~~input.c:136:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while'  136 |     while (*s) s++; s--;      |                     ^In file included from render.h:47,                 from input.c:15:input.c: In function 'global_def':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~input.c:200:24: note: in expansion of macro 'agxbuse'  200 |     sym = dclfun(NULL, agxbuse (xb), rhs);      |                        ^~~~~~~  CC       pointset.lo  CC       postproc.lo  CC       routespl.lo  CC       splines.lo  CC       psusershape.lopsusershape.c: In function 'user_init':psusershape.c:49:30: warning: variable 'rc' set but not used [-Wunused-but-set-variable]   49 |     int saw_bb, must_inline, rc;      |                              ^~In file included from render.h:47,                 from psusershape.c:20:psusershape.c: In function 'ps_string':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~psusershape.c:303:5: note: in expansion of macro 'agxbputc'  303 |     agxbputc (&xb, RPAREN);      |     ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~psusershape.c:305:9: note: in expansion of macro 'agxbuse'  305 |     s = agxbuse(&xb);      |         ^~~~~~~psusershape.c:268:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]  268 |     int rc;      |         ^~  CC       timing.lo  CC       labels.lolabels.c: In function 'xml_url_string':labels.c:561:21: warning: variable 'prev' set but not used [-Wunused-but-set-variable]  561 |     char *p, *sub, *prev = NULL;      |                     ^~~~  CC       ns.lo  CC       shapes.lo  CC       utils.loutils.c: In function 'chkPort':utils.c:690:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]  690 |     else      |     ^~~~utils.c:692:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'  692 |         pt.name = s;      |         ^~In file included from render.h:47,                 from utils.c:14:utils.c: In function 'clustNode':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~utils.c:950:5: note: in expansion of macro 'agxbputc'  950 |     agxbputc(xb, ':');      |     ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~utils.c:954:29: note: in expansion of macro 'agxbuse'  954 |     cn = agnode(agroot(cg), agxbuse(xb));      |                             ^~~~~~~utils.c: In function 'scanEntity':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~utils.c:1359:5: note: in expansion of macro 'agxbputc' 1359 |     agxbputc(xb, '&');      |     ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~utils.c:1369:5: note: in expansion of macro 'agxbputc' 1369 |     agxbputc(xb, '#');      |     ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~utils.c:1371:5: note: in expansion of macro 'agxbputc' 1371 |     agxbputc(xb, ';');      |     ^~~~~~~~utils.c: In function 'htmlEntityUTF8':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~utils.c:1515:18: note: in expansion of macro 'agxbuse' 1515 |     ns = strdup (agxbuse(&xb));      |                  ^~~~~~~utils.c:1456:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1456 |     int rc;      |         ^~utils.c: In function 'latin1ToUTF8':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~utils.c:1555:18: note: in expansion of macro 'agxbuse' 1555 |     ns = strdup (agxbuse(&xb));      |                  ^~~~~~~utils.c:1531:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1531 |     int rc;      |         ^~utils.c: In function 'utf8ToLatin1':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~utils.c:1587:18: note: in expansion of macro 'agxbuse' 1587 |     ns = strdup (agxbuse(&xb));      |                  ^~~~~~~utils.c:1573:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1573 |     int rc;      |         ^~  CC       geom.lo  CC       output.loIn file included from render.h:47,                 from output.c:14:output.c: In function 'attach_attrs_and_arrows':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~output.c:350:29: note: in expansion of macro 'agxbuse'  350 |             agset(n, "pos", agxbuse(&xb));      |                             ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~output.c:373:31: note: in expansion of macro 'agxbuse'  373 |             agset(n, "rects", agxbuse(&xb));      |                               ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~output.c:391:25: note: in expansion of macro 'agxbputc'  391 |                         agxbputc(&xb, ' ');      |                         ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~output.c:403:46: note: in expansion of macro 'agxbuse'  403 |                 agxset(n, N_vertices->index, agxbuse(&xb));      |                                              ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~output.c:417:25: note: in expansion of macro 'agxbputc'  417 |                         agxbputc(&xb, ';');      |                         ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~output.c:434:29: note: in expansion of macro 'agxbputc'  434 |                             agxbputc(&xb, ' ');      |                             ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~output.c:440:33: note: in expansion of macro 'agxbuse'  440 |                 agset(e, "pos", agxbuse(&xb));      |                                 ^~~~~~~  CC       emit.loIn file included from render.h:47,                 from emit.c:25:emit.c: In function 'getObjId':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~emit.c:212:9: note: in expansion of macro 'agxbputc'  212 |         agxbputc (xb, '_');      |         ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~emit.c:218:12: note: in expansion of macro 'agxbuse'  218 |     return agxbuse(xb);      |            ^~~~~~~emit.c: In function 'emit_xdot':emit.c:941:11: warning: variable 'fontname' set but not used [-Wunused-but-set-variable]  941 |     char* fontname;      |           ^~~~~~~~emit.c:940:12: warning: variable 'fontsize' set but not used [-Wunused-but-set-variable]  940 |     double fontsize;      |            ^~~~~~~~emit.c: In function 'selectedlayer':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~emit.c:1152:22: note: in expansion of macro 'agxbuse' 1152 |     w1 = w0 = strtok(agxbuse(&xb), gvc->layerDelims);      |                      ^~~~~~~emit.c: In function 'nodeIntersect':emit.c:2247:11: warning: variable 'target' set but not used [-Wunused-but-set-variable] 2247 |     char* target;      |           ^~~~~~emit.c:2246:11: warning: variable 'tooltip' set but not used [-Wunused-but-set-variable] 2246 |     char* tooltip;      |           ^~~~~~~emit.c: In function 'xdotBB':emit.c:2474:12: warning: variable 'sz' set but not used [-Wunused-but-set-variable] 2474 |     pointf sz;      |            ^~emit.c: In function 'style_token':emit.c:3262:16: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 3262 |     int token, rc;      |                ^~emit.c: In function 'parse_style':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~emit.c:3356:17: note: in expansion of macro 'agxbputc' 3356 |                 agxbputc(&ps_xb, '\0'); /* terminate previous */      |                 ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~emit.c:3359:29: note: in expansion of macro 'agxbuse' 3359 |             agxbput(&ps_xb, agxbuse(&xb));      |                             ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~emit.c:3360:13: note: in expansion of macro 'agxbputc' 3360 |             agxbputc(&ps_xb, '\0');      |             ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~emit.c:3372:11: note: in expansion of macro 'agxbuse' 3372 |     (void)agxbuse(&ps_xb);              /* adds final '\0' to buffer */      |           ^~~~~~~emit.c: In function 'getObjId':emit.c:215:5: warning: 'idnum' may be used uninitialized [-Wmaybe-uninitialized]  215 |     sprintf (buf, "%ld", idnum);      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~emit.c:182:10: note: 'idnum' was declared here  182 |     long idnum;      |          ^~~~~emit.c:214:5: warning: 'pfx' may be used uninitialized [-Wmaybe-uninitialized]  214 |     agxbput (xb, pfx);      |     ^~~~~~~~~~~~~~~~~emit.c:183:11: note: 'pfx' was declared here  183 |     char* pfx;      |           ^~~emit.c: In function 'xdotBB':emit.c:2515:18: warning: 'fontsize' may be used uninitialized [-Wmaybe-uninitialized] 2515 |             sz = textsize (g, op->para, fontname, fontsize);      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~emit.c:2471:12: note: 'fontsize' was declared here 2471 |     double fontsize;      |            ^~~~~~~~emit.c:2515:18: warning: 'fontname' may be used uninitialized [-Wmaybe-uninitialized] 2515 |             sz = textsize (g, op->para, fontname, fontsize);      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~emit.c:2472:11: note: 'fontname' was declared here 2472 |     char* fontname;      |           ^~~~~~~~In function 'multicolor',    inlined from 'emit_edge_graphics' at emit.c:1814:10,    inlined from 'emit_edge' at emit.c:2389:2,    inlined from 'emit_edge' at emit.c:2350:13:emit.c:1776:13: warning: 'endcolor' may be used uninitialized [-Wmaybe-uninitialized] 1776 |             gvrender_set_fillcolor(job, endcolor);      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~emit.c: In function 'emit_edge':emit.c:1723:11: note: 'endcolor' was declared here 1723 |     char* endcolor;      |           ^~~~~~~~In function 'emit_edge_graphics',    inlined from 'emit_edge' at emit.c:2389:2,    inlined from 'emit_edge' at emit.c:2350:13:emit.c:1913:16: warning: 'bz.sflag' may be used uninitialized [-Wmaybe-uninitialized] 1913 |             if (bz.sflag) {      |                ^emit.c: In function 'emit_edge':emit.c:1792:12: note: 'bz.sflag' was declared here 1792 |     bezier bz;      |            ^~In function 'emit_edge_graphics',    inlined from 'emit_edge' at emit.c:2389:2,    inlined from 'emit_edge' at emit.c:2350:13:emit.c:1921:17: warning: 'bz.list' may be used uninitialized [-Wmaybe-uninitialized] 1921 |                 arrow_gen(job, EMIT_TDRAW, bz.sp, bz.list[0],      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1922 |                         arrowsize, penwidth, bz.sflag);      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~emit.c: In function 'emit_edge':emit.c:1792:12: note: 'bz.list' was declared here 1792 |     bezier bz;      |            ^~In function 'emit_edge_graphics',    inlined from 'emit_edge' at emit.c:2389:2,    inlined from 'emit_edge' at emit.c:2350:13:emit.c:1924:16: warning: 'bz.eflag' may be used uninitialized [-Wmaybe-uninitialized] 1924 |             if (bz.eflag) {      |                ^emit.c: In function 'emit_edge':emit.c:1792:12: note: 'bz.eflag' was declared here 1792 |     bezier bz;      |            ^~In function 'emit_edge_graphics',    inlined from 'emit_edge' at emit.c:2389:2,    inlined from 'emit_edge' at emit.c:2350:13:emit.c:1932:58: warning: 'bz.size' may be used uninitialized [-Wmaybe-uninitialized] 1932 |                 arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1],      |                                                          ^emit.c: In function 'emit_edge':emit.c:1792:12: note: 'bz.size' was declared here 1792 |     bezier bz;      |            ^~  CCLD     libcommon_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/common'make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/common'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/common'Making install in packmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/pack'  CC       ccomps.lo  CC       pack.lopack.c: In function 'putGraphs':pack.c:953:12: warning: 'pts' may be used uninitialized [-Wmaybe-uninitialized]  953 |     return pts;      |            ^~~pack.c:920:12: note: 'pts' was declared here  920 |     point* pts;      |            ^~~  CCLD     libpack_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/pack'make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 pack.3 '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 pack.3.pdf '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 pack.h '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/pack'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/pack'Making install in xdotmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'  CC       xdot.loxdot.c: In function 'sprintXDot':xdot.c:537:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]  537 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~xdot.c:538:21: note: in expansion of macro 'agxbputc'  538 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~xdot.c:606:16: note: in expansion of macro 'agxbuse'  606 |     s = strdup(agxbuse(&xb));      |                ^~~~~~~  CCLD     libxdot.la  CCLD     libxdot_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libxdot.la '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib'libtool: install: /usr/bin/install -c .libs/libxdot.lai /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.lalibtool: install: /usr/bin/install -c .libs/libxdot.a /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.alibtool: finish: PATH="/home/biocbuild/.pixi/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/share/Modules/bin:/usr/local/ensembl-vep:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/bioconductor/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/bioconductor/openbabel-3.1.1/bin:/opt/meme/bin:/home/biocbuild/dotnet:/opt/meme/libexec/meme-5.5.5:/home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin:/home/biocbuild/bioconductor/quarto-1.7.32/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib----------------------------------------------------------------------Libraries have been installed in:   /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/libIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify the full pathname of the library, or use the `-LLIBDIR'flag during linking and do at least one of the following:   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable     during execution   - add LIBDIR to the `LD_RUN_PATH' environment variable     during linking   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag   - have your system administrator add LIBDIR to `/etc/ld.so.conf'See any operating system documentation about shared libraries formore information, such as the ld(1) and ld.so(8) manual pages.---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 xdot.3 '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 xdot.3.pdf '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libxdot.pc '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 xdot.h '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'Making install in gvcmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'  CC       gvrender.lo  CC       gvlayout.lo  CC       gvdevice.loIn file included from ../../lib/common/types.h:18,                 from gvplugin_device.h:17,                 from gvdevice.c:55:gvdevice.c: In function 'gvfwrite':gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]  269 |     assert(size = sizeof(char));      |            ^~~~  CC       gvloadimage.lo  CC       gvcontext.lo  CC       gvjobs.lo  CC       gvevent.lo  CC       gvplugin.loIn file included from gvplugin.c:23:gvplugin.c: In function 'gvplugin_list':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gvplugin.c:392:17: note: in expansion of macro 'agxbputc'  392 |                 agxbputc(&xb,' '); agxbput(&xb, (*pnext)->typestr);      |                 ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gvplugin.c:393:17: note: in expansion of macro 'agxbputc'  393 |                 agxbputc(&xb,':'); agxbput(&xb, (*pnext)->package->name);      |                 ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gvplugin.c:410:17: note: in expansion of macro 'agxbputc'  410 |                 agxbputc(&xb,' '); agxbput(&xb, q);      |                 ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvplugin.c:423:14: note: in expansion of macro 'agxbuse'  423 |         bp = agxbuse(&xb);      |              ^~~~~~~  CC       gvconfig.lo  CC       gvtextlayout.lo  CC       gvusershape.logvusershape.c: In function 'gvusershape_open':gvusershape.c:415:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]  415 |                 if (!(us->data = (void*)find_user_shape(us->name)))      |                 ^~gvusershape.c:417:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'  417 |                     free(us);      |                     ^~~~  CC       gvc.lo  CCLD     libgvc.la  CCLD     libgvc_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvc.la '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib'libtool: install: /usr/bin/install -c .libs/libgvc.lai /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.lalibtool: install: /usr/bin/install -c .libs/libgvc.a /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.alibtool: finish: PATH="/home/biocbuild/.pixi/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/share/Modules/bin:/usr/local/ensembl-vep:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/bioconductor/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/bioconductor/openbabel-3.1.1/bin:/opt/meme/bin:/home/biocbuild/dotnet:/opt/meme/libexec/meme-5.5.5:/home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin:/home/biocbuild/bioconductor/quarto-1.7.32/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib----------------------------------------------------------------------Libraries have been installed in:   /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/libIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify the full pathname of the library, or use the `-LLIBDIR'flag during linking and do at least one of the following:   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable     during execution   - add LIBDIR to the `LD_RUN_PATH' environment variable     during linking   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag   - have your system administrator add LIBDIR to `/etc/ld.so.conf'See any operating system documentation about shared libraries formore information, such as the ld(1) and ld.so(8) manual pages.---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 gvc.3 '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 gvc.3.pdf '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libgvc.pc '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 gvc.h gvcext.h gvplugin.h gvcjob.h gvcommon.h gvplugin_render.h gvplugin_layout.h gvconfig.h gvplugin_textlayout.h gvplugin_device.h gvplugin_loadimage.h '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'Making install in circogenmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'  CC       circularinit.lo  CC       nodelist.lo  CC       block.lo  CC       edgelist.lo  CC       circular.lo  CC       deglist.lo  CC       blocktree.lo  CC       blockpath.lo  CC       circpos.loIn function 'positionChildren',    inlined from 'position' at circpos.c:421:2,    inlined from 'doBlock' at circpos.c:468:6:circpos.c:338:20: warning: 'midAngle' may be used uninitialized [-Wmaybe-uninitialized]  338 |         PSI(pi->n) = midAngle;circpos.c: In function 'doBlock':circpos.c:264:39: note: 'midAngle' was declared here  264 |     double mindistAngle, rotateAngle, midAngle;      |                                       ^~~~~~~~  CC       nodeset.lo  CCLD     libcircogen_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'Making install in dotgenmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'  CC       acyclic.lo  CC       class1.lo  CC       class2.lo  CC       cluster.lo  CC       compound.lo  CC       conc.lo  CC       decomp.lo  CC       fastgr.lo  CC       flat.lo  CC       dotinit.lo  CC       mincross.loIn function 'balanceNodes',    inlined from 'balance' at mincross.c:506:3,    inlined from 'mincross.constprop' at mincross.c:638:6:mincross.c:414:12: warning: 'sepIndex' may be used uninitialized [-Wmaybe-uninitialized]  414 |     for (i = sepIndex - 1; i >= 0; i--) {      |          ~~^~~~~~~~~~~~~~mincross.c: In function 'mincross.constprop':mincross.c:374:9: note: 'sepIndex' was declared here  374 |     int sepIndex;      |         ^~~~~~~~  CC       position.lo  CC       rank.lo  CC       sameport.lo  CC       dotsplines.lodotsplines.c: In function 'makeLineEdge':dotsplines.c:1604:30: warning: right-hand operand of comma expression has no effect [-Wunused-value] 1604 |         lp = ED_label(e)->pos, lp;      |                              ^dotsplines.c: In function 'completeregularpath':dotsplines.c:1866:9: warning: variable 'pn' set but not used [-Wunused-but-set-variable] 1866 |     int pn;      |         ^~dotsplines.c:1865:13: warning: variable 'pp' set but not used [-Wunused-but-set-variable] 1865 |     pointf *pp;      |             ^~In function 'makeSimpleFlatLabels',    inlined from 'make_flat_adj_edges' at dotsplines.c:1117:6,    inlined from 'make_flat_edge' at dotsplines.c:1457:2,    inlined from '_dot_splines' at dotsplines.c:440:6:dotsplines.c:997:25: warning: 'lminx' may be used uninitialized [-Wmaybe-uninitialized]  997 |             points[7].x = lminx;      |             ~~~~~~~~~~~~^~~~~~~dotsplines.c: In function '_dot_splines':dotsplines.c:882:12: note: 'lminx' was declared here  882 |     double lminx, lmaxx;      |            ^~~~~In function 'makeSimpleFlatLabels',    inlined from 'make_flat_adj_edges' at dotsplines.c:1117:6,    inlined from 'make_flat_edge' at dotsplines.c:1457:2,    inlined from '_dot_splines' at dotsplines.c:440:6:dotsplines.c:993:25: warning: 'lmaxx' may be used uninitialized [-Wmaybe-uninitialized]  993 |             points[5].x = lmaxx;      |             ~~~~~~~~~~~~^~~~~~~dotsplines.c: In function '_dot_splines':dotsplines.c:882:19: note: 'lmaxx' was declared here  882 |     double lminx, lmaxx;      |                   ^~~~~dotsplines.c:488:9: warning: 'edges' may be used uninitialized [-Wmaybe-uninitialized]  488 |         free(edges);      |         ^~~~~~~~~~~dotsplines.c:268:50: note: 'edges' was declared here  268 |     edge_t *e, *e0, *e1, *ea, *eb, *le0, *le1, **edges;      |                                                  ^~~~~dotsplines.c:489:15: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized]  489 |         free(P->boxes);      |              ~^~~~~~~dotsplines.c:269:11: note: 'P' was declared here  269 |     path *P;      |           ^  CC       aspect.loaspect.c: In function 'computeCombiAR':aspect.c:1614:12: warning: variable 'maxLayerIndex' set but not used [-Wunused-but-set-variable] 1614 |     int i, maxLayerIndex;      |            ^~~~~~~~~~~~~In function 'reduceMaxWidth2',    inlined from 'applyPacking2' at aspect.c:1088:5,    inlined from 'rank3' at aspect.c:1824:2:aspect.c:736:25: warning: 'maxLayerIndex' may be used uninitialized [-Wmaybe-uninitialized]  736 |     qsort(layerWidthInfo[maxLayerIndex].nodeGroupsInLayer,      |                         ^aspect.c: In function 'rank3':aspect.c:702:9: note: 'maxLayerIndex' was declared here  702 |     int maxLayerIndex;      |         ^~~~~~~~~~~~~In function 'reduceMaxWidth2',    inlined from 'applyPacking2' at aspect.c:1088:5,    inlined from 'rank3' at aspect.c:1824:2:aspect.c:749:8: warning: 'nextMaxWidth' may be used uninitialized [-Wmaybe-uninitialized]  749 |     if (nextMaxWidth <= layerWidthInfo[maxLayerIndex].width / 4      |        ^aspect.c: In function 'rank3':aspect.c:703:12: note: 'nextMaxWidth' was declared here  703 |     double nextMaxWidth;      |            ^~~~~~~~~~~~  CCLD     libdotgen_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'Making install in fdpgenmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'  CC       comp.lo  CC       dbg.lo  CC       grid.lo  CC       fdpinit.lo  CC       layout.lo  CC       tlayout.lo  CC       xlayout.lo  CC       clusteredges.lo  CCLD     libfdpgen_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'Making install in neatogenmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'  CC       adjust.loadjust.c: In function 'getSizes':adjust.c:674:48: warning: 'nedge_nodes' may be used uninitialized [-Wmaybe-uninitialized]  674 |         if (elabels && IS_LNODE(n)) nedge_nodes++;      |                                     ~~~~~~~~~~~^~adjust.c:670:12: note: 'nedge_nodes' was declared here  670 |     int i, nedge_nodes;      |            ^~~~~~~~~~~adjust.c: In function 'removeOverlapWith':adjust.c:1045:9: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] 1045 |     int ret;      |         ^~~  CC       circuit.lo  CC       edges.lo  CC       geometry.lo  CC       heap.lo  CC       hedges.lo  CC       info.lo  CC       neatoinit.lo  CC       legal.lo  CC       lu.lo  CC       matinv.lo  CC       memory.lo  CC       poly.lo  CC       printvis.lo  CC       site.lo  CC       solve.lo  CC       neatosplines.loneatosplines.c: In function 'makeObstacle':neatosplines.c:363:13: warning: variable 'desc' set but not used [-Wunused-but-set-variable]  363 |     epsf_t *desc;      |             ^~~~neatosplines.c: In function '_spline_edges':neatosplines.c:603:15: warning: unused variable 'rtr' [-Wunused-variable]  603 |     router_t* rtr = 0;      |               ^~~  CC       stuff.lo  CC       voronoi.lovoronoi.c: In function 'voronoi':voronoi.c:46:49: warning: 'newintstar.y' may be used uninitialized [-Wmaybe-uninitialized]   45 |         if (newsite != (struct Site *) NULL && (PQempty()      |                                                 ~~~~~~~~~   46 |                                                 || newsite->coord.y <      |                                                 ^~~~~~~~~~~~~~~~~~~~~   47 |                                                 newintstar.y      |                                                 ~~~~~~~~~~~~voronoi.c:26:11: note: 'newintstar.y' was declared here   26 |     Point newintstar;      |           ^~~~~~~~~~  CC       stress.lostress.c: In function 'mdsModel':stress.c:1383:19: warning: 'delta' may be used uninitialized [-Wmaybe-uninitialized] 1383 |             delta += abs(Dij[i*nG + j - shift] - graph[i].ewgts[e]);      |             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~stress.c:1370:12: note: 'delta' was declared here 1370 |     double delta;      |            ^~~~~  CC       kkutils.lo  CC       matrix_ops.lo  CC       embed_graph.lo  CC       dijkstra.lo  CC       conjgrad.lo  CC       pca.lo  CC       closest.lo  CC       bfs.lo  CC       constraint.lo  CC       quad_prog_solve.lo  CC       smart_ini_x.lo  CC       constrained_majorization.lo  CC       opt_arrangement.lo  CC       overlap.lo  CC       call_tri.lo  CC       compute_hierarchy.lo  CC       delaunay.lo  CC       multispline.lo  CCLD     libneatogen_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'Making install in twopigenmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'  CC       twopiinit.lo  CC       circle.loIn function 'getRankseps',    inlined from 'setAbsolutePos' at circle.c:299:15,    inlined from 'circleLayout' at circle.c:368:5:circle.c:285:12: warning: 'delx' may be used uninitialized [-Wmaybe-uninitialized]  285 |         xf += delx;      |         ~~~^~~~~~~circle.c: In function 'circleLayout':circle.c:268:20: note: 'delx' was declared here  268 |     double xf = 0, delx, d;      |                    ^~~~  CCLD     libtwopigen_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'Making install in sfdpgenmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'  CC       sfdpinit.lo  CC       spring_electrical.lospring_electrical.c: In function 'rotate':spring_electrical.c:1850:8: warning: variable 'y' set but not used [-Wunused-but-set-variable] 1850 |   real y[4], axis[2], center[2], x0, x1;      |        ^  CC       LinkedList.lo  CC       sparse_solve.lo  CC       post_process.lopost_process.c: In function 'StressMajorizationSmoother2_new':post_process.c:110:36: warning: variable 'dd' set but not used [-Wunused-but-set-variable]  110 |   real *avg_dist, diag_d, diag_w, *dd, dist, s = 0, stop = 0, sbot = 0;      |                                    ^~post_process.c: In function 'StressMajorizationSmoother_smooth':post_process.c:578:102: warning: variable 'res' set but not used [-Wunused-but-set-variable]  578 |   real *w, *dd, *d, *y = NULL, *x0 = NULL, *x00 = NULL, diag, diff = 1, *lambda = sm->lambda, maxit, res, alpha = 0., M = 0.;      |                                                                                                      ^~~post_process.c:578:9: warning: variable 'w' set but not used [-Wunused-but-set-variable]  578 |   real *w, *dd, *d, *y = NULL, *x0 = NULL, *x00 = NULL, diag, diff = 1, *lambda = sm->lambda, maxit, res, alpha = 0., M = 0.;      |         ^post_process.c:577:32: warning: variable 'jw' set but not used [-Wunused-but-set-variable]  577 |   int i, j, m, *id, *jd, *iw, *jw, idiag, flag = 0, iter = 0;      |                                ^~post_process.c:577:27: warning: variable 'iw' set but not used [-Wunused-but-set-variable]  577 |   int i, j, m, *id, *jd, *iw, *jw, idiag, flag = 0, iter = 0;      |                           ^~post_process.c: In function 'TriangleSmoother_new':post_process.c:698:68: warning: variable 'jd' set but not used [-Wunused-but-set-variable]  698 |   int i, j, k, m = A->m, *ia = A->ia, *ja = A->ja, *iw, *jw, *id, *jd, jdiag, nz;      |                                                                    ^~post_process.c:698:63: warning: variable 'id' set but not used [-Wunused-but-set-variable]  698 |   int i, j, k, m = A->m, *ia = A->ia, *ja = A->ja, *iw, *jw, *id, *jd, jdiag, nz;      |                                                               ^~  CC       stress_model.lo  CC       uniform_stress.louniform_stress.c: In function 'uniform_stress':uniform_stress.c:112:8: warning: variable 'res' set but not used [-Wunused-but-set-variable]  112 |   real res;      |        ^~~  CC       QuadTree.lo  CC       Multilevel.loMultilevel.c: In function 'maximal_independent_vertex_set':Multilevel.c:87:30: warning: variable 'n' set but not used [-Wunused-but-set-variable]   87 |   int i, ii, j, *ia, *ja, m, n, *p = NULL;      |                              ^Multilevel.c: In function 'maximal_independent_vertex_set_RS':Multilevel.c:138:57: warning: variable 'removed' set but not used [-Wunused-but-set-variable]  138 |   int i, jj, ii, *p = NULL, j, k, *ia, *ja, m, n, gain, removed, nf = 0;      |                                                         ^~~~~~~Multilevel.c:138:48: warning: variable 'n' set but not used [-Wunused-but-set-variable]  138 |   int i, jj, ii, *p = NULL, j, k, *ia, *ja, m, n, gain, removed, nf = 0;      |                                                ^Multilevel.c: In function 'maximal_independent_edge_set_heavest_edge_pernode_leaves_first':Multilevel.c:327:30: warning: variable 'n' set but not used [-Wunused-but-set-variable]  327 |   int i, ii, j, *ia, *ja, m, n, *p = NULL, q;      |                              ^Multilevel.c: In function 'maximal_independent_edge_set_heavest_edge_pernode_supernodes_first':Multilevel.c:502:30: warning: variable 'n' set but not used [-Wunused-but-set-variable]  502 |   int i, ii, j, *ia, *ja, m, n, *p = NULL;      |                              ^Multilevel.c: In function 'maximal_independent_edge_set_heavest_cluster_pernode_leaves_first':Multilevel.c:646:30: warning: variable 'n' set but not used [-Wunused-but-set-variable]  646 |   int i, ii, j, *ia, *ja, m, n, *p = NULL, q, iv;      |                              ^  CC       PriorityQueue.lo  CCLD     libsfdpgen_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'Making install in osagemake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/osage'  CC       osageinit.lo  CCLD     libosage_C.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/osage'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/osage'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib/osage'make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib'make[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/lib'Making install in pluginmake[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin'Making install in coremake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/core'  CC       gvplugin_core.lo  CC       gvrender_core_dot.loIn file included from gvrender_core_dot.c:32:gvrender_core_dot.c: In function 'xdot_str':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gvrender_core_dot.c:100:5: note: in expansion of macro 'agxbputc'  100 |     agxbputc(xbufs[emit_state], ' ');      |     ^~~~~~~~gvrender_core_dot.c: In function 'xdot_points':gvrender_core_dot.c:107:12: warning: variable 'rc' set but not used [-Wunused-but-set-variable]  107 |     int i, rc;      |            ^~gvrender_core_dot.c: In function 'xdot_style':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gvrender_core_dot.c:162:13: note: in expansion of macro 'agxbputc'  162 |             agxbputc(&xbuf, '(');      |             ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gvrender_core_dot.c:166:21: note: in expansion of macro 'agxbputc'  166 |                     agxbputc(&xbuf, ',');      |                     ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gvrender_core_dot.c:172:13: note: in expansion of macro 'agxbputc'  172 |             agxbputc(&xbuf, ')');      |             ^~~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:174:30: note: in expansion of macro 'agxbuse'  174 |         xdot_str (job, "S ", agxbuse(&xbuf));      |                              ^~~~~~~gvrender_core_dot.c: In function 'xdot_end_node':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:186:38: note: in expansion of macro 'agxbuse'  186 |         agxset(n, xd->n_draw->index, agxbuse(xbufs[EMIT_NDRAW]));      |                                      ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:192:40: note: in expansion of macro 'agxbuse'  192 |         agxset(n, xd->n_l_draw->index, agxbuse(xbufs[EMIT_NLABEL]));      |                                        ^~~~~~~gvrender_core_dot.c: In function 'xdot_end_edge':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:206:38: note: in expansion of macro 'agxbuse'  206 |         agxset(e, xd->e_draw->index, agxbuse(xbufs[EMIT_EDRAW]));      |                                      ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:212:38: note: in expansion of macro 'agxbuse'  212 |         agxset(e, xd->t_draw->index, agxbuse(xbufs[EMIT_TDRAW]));      |                                      ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:218:38: note: in expansion of macro 'agxbuse'  218 |         agxset(e, xd->h_draw->index, agxbuse(xbufs[EMIT_HDRAW]));      |                                      ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:224:39: note: in expansion of macro 'agxbuse'  224 |         agxset(e, xd->e_l_draw->index,agxbuse(xbufs[EMIT_ELABEL]));      |                                       ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:230:39: note: in expansion of macro 'agxbuse'  230 |         agxset(e, xd->tl_draw->index, agxbuse(xbufs[EMIT_TLABEL]));      |                                       ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:236:39: note: in expansion of macro 'agxbuse'  236 |         agxset(e, xd->hl_draw->index, agxbuse(xbufs[EMIT_HLABEL]));      |                                       ^~~~~~~gvrender_core_dot.c: In function 'xdot_end_cluster':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:289:42: note: in expansion of macro 'agxbuse'  289 |     agxset(cluster_g, xd->g_draw->index, agxbuse(xbufs[EMIT_CDRAW]));      |                                          ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:295:48: note: in expansion of macro 'agxbuse'  295 |         agxset(cluster_g, xd->g_l_draw->index, agxbuse(xbufs[EMIT_CLABEL]));      |                                                ^~~~~~~gvrender_core_dot.c: In function 'xdot_end_graph':../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:436:38: note: in expansion of macro 'agxbuse'  436 |         agxset(g, xd->g_draw->index, agxbuse(xbufs[EMIT_GDRAW]));      |                                      ^~~~~~~../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]   68 |           (int)(*(X)->ptr++ = ((unsigned char)C)))      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'   74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))      |                     ^~~~~~~~gvrender_core_dot.c:444:40: note: in expansion of macro 'agxbuse'  444 |         agxset(g, xd->g_l_draw->index, agxbuse(xbufs[EMIT_GLABEL]));      |                                        ^~~~~~~  CC       gvrender_core_fig.lo  CC       gvrender_core_map.lo  CC       gvrender_core_ps.lo  CC       gvrender_core_svg.lo  CC       gvrender_core_tk.logvrender_core_tk.c: In function 'tkgen_print_tags':gvrender_core_tk.c:58:18: warning: variable 'ObjId' set but not used [-Wunused-but-set-variable]   58 |     unsigned int ObjId;      |                  ^~~~~gvrender_core_tk.c:57:21: warning: variable 'ObjPart' set but not used [-Wunused-but-set-variable]   57 |     char *ObjType, *ObjPart;      |                     ^~~~~~~  CC       gvrender_core_vml.logvrender_core_vml.c: In function 'vml_ellipse':gvrender_core_vml.c:452:38: warning: variable 'bottom' set but not used [-Wunused-but-set-variable]  452 |     double dx, dy, left, right, top, bottom;      |                                      ^~~~~~gvrender_core_vml.c:452:26: warning: variable 'right' set but not used [-Wunused-but-set-variable]  452 |     double dx, dy, left, right, top, bottom;      |                          ^~~~~  CC       gvloadimage_core.logvloadimage_core.c:19:22: warning: extra tokens at end of #include directive   19 | #include <unistd.h>  # for read() declaration      |                      ^  CCLD     libgvplugin_core_C.la  CCLD     libgvplugin_core.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/core' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_core.la '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.lalibtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.alibtool: finish: PATH="/home/biocbuild/.pixi/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/share/Modules/bin:/usr/local/ensembl-vep:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/bioconductor/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/bioconductor/openbabel-3.1.1/bin:/opt/meme/bin:/home/biocbuild/dotnet:/opt/meme/libexec/meme-5.5.5:/home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin:/home/biocbuild/bioconductor/quarto-1.7.32/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz----------------------------------------------------------------------Libraries have been installed in:   /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphvizIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify the full pathname of the library, or use the `-LLIBDIR'flag during linking and do at least one of the following:   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable     during execution   - add LIBDIR to the `LD_RUN_PATH' environment variable     during linking   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag   - have your system administrator add LIBDIR to `/etc/ld.so.conf'See any operating system documentation about shared libraries formore information, such as the ld(1) and ld.so(8) manual pages.----------------------------------------------------------------------make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/core'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/core'Making install in dot_layoutmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'  CC       gvplugin_dot_layout.lo  CC       gvlayout_dot_layout.lo  CCLD     libgvplugin_dot_layout_C.la  CCLD     libgvplugin_dot_layout.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_dot_layout.la '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.lalibtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.alibtool: finish: PATH="/home/biocbuild/.pixi/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/share/Modules/bin:/usr/local/ensembl-vep:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/bioconductor/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/bioconductor/openbabel-3.1.1/bin:/opt/meme/bin:/home/biocbuild/dotnet:/opt/meme/libexec/meme-5.5.5:/home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin:/home/biocbuild/bioconductor/quarto-1.7.32/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz----------------------------------------------------------------------Libraries have been installed in:   /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphvizIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify the full pathname of the library, or use the `-LLIBDIR'flag during linking and do at least one of the following:   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable     during execution   - add LIBDIR to the `LD_RUN_PATH' environment variable     during linking   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag   - have your system administrator add LIBDIR to `/etc/ld.so.conf'See any operating system documentation about shared libraries formore information, such as the ld(1) and ld.so(8) manual pages.----------------------------------------------------------------------make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'Making install in neato_layoutmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'  CC       gvplugin_neato_layout.lo  CC       gvlayout_neato_layout.lo  CCLD     libgvplugin_neato_layout_C.la  CCLD     libgvplugin_neato_layout.lamake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_neato_layout.la '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.lalibtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.alibtool: finish: PATH="/home/biocbuild/.pixi/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/share/Modules/bin:/usr/local/ensembl-vep:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/bioconductor/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/bioconductor/openbabel-3.1.1/bin:/opt/meme/bin:/home/biocbuild/dotnet:/opt/meme/libexec/meme-5.5.5:/home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin:/home/biocbuild/bioconductor/quarto-1.7.32/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz----------------------------------------------------------------------Libraries have been installed in:   /home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphvizIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify the full pathname of the library, or use the `-LLIBDIR'flag during linking and do at least one of the following:   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable     during execution   - add LIBDIR to the `LD_RUN_PATH' environment variable     during linking   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag   - have your system administrator add LIBDIR to `/etc/ld.so.conf'See any operating system documentation about shared libraries formore information, such as the ld(1) and ld.so(8) manual pages.----------------------------------------------------------------------make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin'make[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin'make[4]: Nothing to be done for 'install-exec-am'.make[4]: Nothing to be done for 'install-data-am'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz/plugin'make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz'make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz'make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man7' /usr/bin/install -c -m 644 graphviz.7 '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/man/man7' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 graphviz_version.h '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc' /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz'make[1]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/graphviz'cp: -r not specified; omitting directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'cp: -r not specified; omitting directory '/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'checking for stdio.h... yeschecking for stdlib.h... yeschecking for string.h... yeschecking for inttypes.h... yeschecking for stdint.h... yeschecking for strings.h... yeschecking for sys/stat.h... yeschecking for sys/types.h... yeschecking for unistd.h... yeschecking for zlib.h... yeschecking for deflateBound in -lz... yeschecking for library containing pow... -lmchecking for _Bool... yeschecking for stdbool.h that conforms to C99 or later... yeschecking for whether compiler has bool... yesconfigure: Using the following compilation and linking flags for Rgraphvizconfigure:    PKG_CFLAGS= -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphvizconfigure:    PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -lmconfigure:    GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1configure: Compiling using Graphviz version: '2.28.0'.configure: Using bundled Graphviz: 'TRUE'.configure: creating ./config.statusconfig.status: creating R/graphviz_build_version.Rconfig.status: creating src/Makevars** libsusing C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c LL_funcs.c -o LL_funcs.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c Rgraphviz.c -o Rgraphviz.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c RgraphvizInit.c -o RgraphvizInit.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c agopen.c -o agopen.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c agread.c -o agread.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c agwrite.c -o agwrite.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c bezier.c -o bezier.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c buildEdgeList.c -o buildEdgeList.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c buildNodeList.c -o buildNodeList.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c doLayout.c -o doLayout.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c graphvizVersion.c -o graphvizVersion.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.22-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -g -O2  -c init.c -o init.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -lm -L/home/biocbuild/R/R-4.5.0/lib -lRinstalling to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-Rgraphviz/00new/Rgraphviz/libs** R** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (Rgraphviz)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-unknown-linux-gnuR is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> require("Rgraphviz") || stop("unable to load Rgraphviz")Loading required package: RgraphvizLoading required package: graphLoading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,    as.data.frame, basename, cbind, colnames, dirname, do.call,    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,    unsplit, which.max, which.minLoading required package: grid[1] TRUE> BiocGenerics:::testPackage("Rgraphviz")plotting different layout types   dot  .... done   circo  .... done   fdp  .... done   neato  .... done   osage  .... done   twopi  .... doneusing toFile with various device types   canon . done   cmap . done   cmapx . done   cmapx_np . done   dot . done   eps . done   fig . done   gv . done   imap . done   imap_np . done   ismap . done   plain . done   plain-ext . done   ps . done   ps2 . done   svg . done   tk . done   vml . done   xdot . doneRUNIT TEST PROTOCOL -- Fri Dec 12 14:24:07 2025 *********************************************** Number of test functions: 4 Number of errors: 0 Number of failures: 0  1 Test Suite : Rgraphviz RUnit Tests - 4 test functions, 0 errors, 0 failuresNumber of test functions: 4 Number of errors: 0 Number of failures: 0 > > proc.time()   user  system elapsed   1.603   0.072   1.680