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Back toMultiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-12-15 12:07 -0500 (Mon, 15 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble"4882
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble"4673
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"4607
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six"4671
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package2254/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.54.0  (landing page)
Julius Muller
Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025)
git_url: https://git.bioconductor.org/packages/TransView
git_branch: RELEASE_3_22
git_last_commit: 23c9dd4
git_last_commit_date: 2025-10-29 10:12:30 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

BUILD BIN results for TransView on merida1

To the developers/maintainers of the TransView package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TransView.git to reflect on this report. SeeTroubleshooting Build Report for more information.
- Use the followingRenviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. SeeRenviron.bioc for more information.

raw results


Summary

Package: TransView
Version: 1.54.0
Command: rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.54.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R TransView.buildbin-libdir
StartedAt: 2025-12-12 15:58:24 -0500 (Fri, 12 Dec 2025)
EndedAt: 2025-12-12 15:59:02 -0500 (Fri, 12 Dec 2025)
EllapsedTime: 38.8 seconds
RetCode: 0
Status:  OK  
PackageFile: TransView_1.54.0.tgz
PackageFileSize: 2.131MiB

Command output

################################################################################################################################################################## Running command:######   rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.54.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R TransView.buildbin-libdir###############################################################################################################################################################>>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=TransView.buildbin-libdir TransView_1.54.0.tar.gz'>>>>>>> * installing *source* package ‘TransView’ ...** this is package ‘TransView’ version ‘1.54.0’** using staged installation** libsusing C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’using SDK: ‘MacOSX11.3.1.sdk’clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_TransView.c -o R_init_TransView.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bin_density.c -o bin_density.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c construct_dc.c -o construct_dc.oIn file included from construct_dc.c:23:In file included from ./parse_sam.h:13:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include/htslib/sam.h:33:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include/htslib/hts.h:36:/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include/htslib/hts_log.h:76:1: warning: '__format__' attribute argument not supported: Rprintf [-Wignored-attributes]HTS_FORMAT(HTS_PRINTF_FMT, 3, 4);^/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include/htslib/hts_defs.h:101:53: note: expanded from macro 'HTS_FORMAT'#define HTS_FORMAT(type, idx, first) __attribute__((__format__ (type, idx, first)))                                                    ^1 warning generated.clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c parse_sam.c -o parse_sam.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c slice_dc.c -o slice_dc.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c visuals.c -o visuals.oclang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o TransView.so R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -lz -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Users/biocbuild/bbs-3.22-bioc/meat/TransView.buildbin-libdir/00LOCK-TransView/00new/TransView/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 locationWarning in fun(libname, pkgname) :  Package 'TransView' is deprecated and will be removed from Bioconductor  version 3.23** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final locationWarning in fun(libname, pkgname) :  Package 'TransView' is deprecated and will be removed from Bioconductor  version 3.23** testing if installed package keeps a record of temporary installation path* DONE (TransView)>>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR TransView.buildbin-libdir/TransView/libs/TransView.so>>>>>>> >>>>>>> Paths before fix:TransView.buildbin-libdir/TransView/libs/TransView.so:TransView.so (compatibility version 0.0.0, current version 0.0.0)/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)>>>>>>> Fix with install_name_tool:install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "TransView.buildbin-libdir/TransView/libs/TransView.so"install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "TransView.buildbin-libdir/TransView/libs/TransView.so"install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "TransView.buildbin-libdir/TransView/libs/TransView.so">>>>>>> Paths after fix:TransView.buildbin-libdir/TransView/libs/TransView.so:TransView.so (compatibility version 0.0.0, current version 0.0.0)/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
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