Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-26 06:18:12 -0000 (Fri, 26 May 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
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 |
To the developers/maintainers of the motifcounter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifcounter.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1264/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
motifcounter 1.25.0 (landing page) Wolfgang Kopp
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
Package: motifcounter |
Version: 1.25.0 |
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings motifcounter_1.25.0.tar.gz |
StartedAt: 2023-05-26 04:48:50 -0000 (Fri, 26 May 2023) |
EndedAt: 2023-05-26 04:49:03 -0000 (Fri, 26 May 2023) |
EllapsedTime: 13.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: motifcounter.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings motifcounter_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/motifcounter.Rcheck’ * using R version 4.3.0 (2023-04-21) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘motifcounter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘motifcounter’ version ‘1.25.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib: download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib: download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib: download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .zenodo.json These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘motifcounter’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... OK * 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 R 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 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 ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘motifcounter.Rmd’ using ‘UTF-8’... failed to complete the test ERROR Errors in running code in vignettes: when running code in ‘motifcounter.Rmd’ ... > proc.time() user system elapsed 0.183 0.019 0.196 ... incomplete output. Crash? * checking re-building of vignette outputs ... OK * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: * checking PDF version of manual without index ... ERROR * DONE Status: 2 ERRORs, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/motifcounter.Rcheck/00check.log’ for details.
motifcounter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL motifcounter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘motifcounter’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Rbackground.c -o Rbackground.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Rcombinatorial.c -o Rcombinatorial.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Rcompoundpoisson.c -o Rcompoundpoisson.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Rminmaxscore.c -o Rminmaxscore.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Roption.c -o Roption.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Roverlap.c -o Roverlap.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Rscore1d.c -o Rscore1d.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Rsequence.c -o Rsequence.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c Rsimulate.c -o Rsimulate.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c background.c -o background.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c combinatorial.c -o combinatorial.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c compoundpoisson.c -o compoundpoisson.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c markovchain.c -o markovchain.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c markovchain_single.c -o markovchain_single.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c matrix.c -o matrix.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c mdist_register.c -o mdist_register.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c minmaxscore.c -o minmaxscore.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c overlap.c -o overlap.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c score1d.c -o score1d.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c score2d.c -o score2d.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c scorefunctions.c -o scorefunctions.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c sequence.c -o sequence.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -c simulate.c -o simulate.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -fopenmp -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-motifcounter/00new/motifcounter/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 (motifcounter)