Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:11 -0000 (Fri, 26 May 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 maftools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maftools.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 1087/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maftools 2.17.0 (landing page) Anand Mayakonda
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
Package: maftools |
Version: 2.17.0 |
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:maftools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings maftools_2.17.0.tar.gz |
StartedAt: 2023-05-26 04:46:18 -0000 (Fri, 26 May 2023) |
EndedAt: 2023-05-26 04:46:36 -0000 (Fri, 26 May 2023) |
EllapsedTime: 18.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: maftools.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:maftools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings maftools_2.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/maftools.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 ‘maftools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘maftools’ version ‘2.17.0’ * package encoding: UTF-8 * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘maftools’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 11.0Mb sub-directories of 1Mb or more: extdata 6.0Mb libs 3.9Mb * 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 ... NOTE GNU make is a SystemRequirements. * 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 vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘cancer_hotspots.Rmd’ using ‘UTF-8’... failed to complete the test ‘cnv_analysis.Rmd’ using ‘UTF-8’... failed to complete the test ‘maftools.Rmd’ using ‘UTF-8’... failed to complete the test ‘oncoplots.Rmd’ using ‘UTF-8’... failed to complete the test ERROR Errors in running code in vignettes: when running code in ‘cancer_hotspots.Rmd’ ... > proc.time() user system elapsed 0.179 0.030 0.203 ... incomplete output. Crash? when running code in ‘cnv_analysis.Rmd’ ... > proc.time() user system elapsed 0.169 0.037 0.201 ... incomplete output. Crash? when running code in ‘maftools.Rmd’ ... > proc.time() user system elapsed 0.167 0.038 0.198 ... incomplete output. Crash? when running code in ‘oncoplots.Rmd’ ... > proc.time() user system elapsed 0.167 0.040 0.201 ... incomplete output. Crash? * checking re-building of vignette outputs ... OK * checking PDF version of manual ... ERROR Rd conversion errors: Converting parsed Rd's to LaTeX Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device .Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Warning in close.connection(con) : Problem closing connection: No space left on device Error in writeLines(x, con, useBytes = TRUE, ...) : Error writing to connection: No space left on device * DONE Status: 2 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/maftools.Rcheck/00check.log’ for details.
maftools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL maftools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘maftools’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -c ntcounts.c -o ntcounts.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -c snpcounts.c -o snpcounts.o snpcounts.c: In function ‘snpcounts’: snpcounts.c:56:26: warning: passing argument 1 of ‘countlines’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 56 | int nloci = countlines(bedfile); | ^~~~~~~ snpcounts.c:13:22: note: expected ‘char *’ but argument is of type ‘const char *’ 13 | int countlines(char *filename){ | ~~~~~~^~~~~~~~ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -c somaticfreq.c -o somaticfreq.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o maftools.so ntcounts.o snpcounts.o somaticfreq.o /home/biocbuild/R/R-4.3.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-maftools/00new/maftools/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 (maftools)