Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sRACIPE_2.2.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sRACIPE.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 ‘sRACIPE/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘sRACIPE’ version ‘2.2.0’* package encoding: UTF-8* 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 ‘sRACIPE’ can be installed ... OK* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’* checking C++ specification ... NOTE  Specified C++11: please drop specification unless essential* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... NOTELicense stub is invalid DCF.* 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 dependencies in R code ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTEsracipeSimulate: no visible binding for global variable  ‘configurationTmp’sracipeSimulate: no visible binding for global variable ‘outFileGETmp’sracipeSimulate: no visible binding for global variable  ‘outFileParamsTmp’sracipeSimulate: no visible binding for global variable ‘outFileICTmp’sracipeSimulate: no visible binding for global variable  ‘outFileConvergeTmp’sracipeConvergeDist,RacipeSE: no visible global function definition for  ‘polygon’Undefined global functions or variables:  configurationTmp outFileConvergeTmp outFileGETmp outFileICTmp  outFileParamsTmp polygonConsider adding  importFrom("graphics", "polygon")to your NAMESPACE file.* checking Rd files ... NOTEcheckRd: (-1) sracipeHeatmapSimilarity.Rd:31: Lost braces    31 | If clusterCut is missing, hierarchical clustering using /code{ward.D2}       |                                                              ^checkRd: (-1) sracipeHeatmapSimilarity.Rd:32: Lost braces    32 | and /code{distance  = (1-cor(x, method = "spear"))/2} will be used to        |          ^* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  RacipeSE-class.Rd: SummarizedExperiment  RacipeSE.Rd: SummarizedExperimentPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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 contents of ‘data’ directory ... OK* checking data for non-ASCII characters ... OK* checking LazyData ... OK* checking data for ASCII and uncompressed saves ... 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 compiled code ... NOTENote: information on .o files is not available* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                  user system elapsedsracipeSimulate 29.238  0.104  29.399* 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: 6 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/sRACIPE.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD INSTALL sRACIPE###############################################################################################################################################################* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’* installing *source* package ‘sRACIPE’ ...** this is package ‘sRACIPE’ version ‘2.2.0’** using staged installation** libsusing C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’using C++11/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c generateThresholds.cpp -o generateThresholds.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c header.cpp -o header.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c limitcycle.cpp -o limitcycle.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c simulateGRC.cpp -o simulateGRC.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c steppers.cpp -o steppers.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c steppersConv.cpp -o steppersConv.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o sRACIPE.so RcppExports.o generateThresholds.o header.o limitcycle.o simulateGRC.o steppers.o steppersConv.o -L/home/biocbuild/R/R-4.5.0/lib -lRinstalling to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-sRACIPE/00new/sRACIPE/libs** R** data*** moving datasets to lazyload DB** 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 (sRACIPE)