Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 |
Package 1210/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylMnM 1.43.0 (landing page) Yan Zhou
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the methylMnM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylMnM.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron 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. See Renviron.bioc for more information. |
Package: methylMnM |
Version: 1.43.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylMnM.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methylMnM_1.43.0.tar.gz |
StartedAt: 2024-07-16 01:38:12 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 01:38:46 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 34.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methylMnM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylMnM.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methylMnM_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/methylMnM.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'methylMnM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'methylMnM' version '1.43.0' * 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 whether package 'methylMnM' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 47.6Mb sub-directories of 1Mb or more: extdata 47.4Mb * 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 dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: 'edgeR' 'statmod' Please remove these calls from your code. Packages in Depends field not imported from: 'edgeR' 'statmod' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CNVnormal: no visible global function definition for 'read.table' MnM.qvalue: no visible global function definition for 'read.table' MnM.qvalue: no visible global function definition for 'write.table' MnM.selectDMR: no visible global function definition for 'quantile' MnM.test: no visible global function definition for 'read.table' MnM.test: no visible global function definition for 'calcNormFactors' MnM.test: no visible global function definition for 'sage.test' MnM.test: no visible global function definition for 'lm' MnM.test: no visible global function definition for 'write.table' countMREbin: no visible global function definition for 'read.table' countMREbin: no visible global function definition for 'count.fields' countMREbin: no visible global function definition for 'write.table' countMREcpgbin: no visible global function definition for 'read.table' countMREcpgbin: no visible global function definition for 'count.fields' countMREcpgbin: no visible global function definition for 'write.table' countMeDIPbin: no visible global function definition for 'read.table' countMeDIPbin: no visible global function definition for 'count.fields' countMeDIPbin: no visible global function definition for 'write.table' countcpgbin: no visible global function definition for 'read.table' countcpgbin: no visible global function definition for 'count.fields' countcpgbin: no visible global function definition for 'write.table' normpdf: no visible global function definition for 'pnorm' removeblacklist: no visible global function definition for 'read.table' Undefined global functions or variables: calcNormFactors count.fields lm pnorm quantile read.table sage.test write.table Consider adding importFrom("stats", "lm", "pnorm", "quantile") importFrom("utils", "count.fields", "read.table", "write.table") to your NAMESPACE file. * 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 compiled code ... NOTE Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/methylMnM/libs/x64/methylMnM.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... 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 * DONE Status: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/methylMnM.Rcheck/00check.log' for details.
methylMnM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL methylMnM ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'methylMnM' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CpGcount.c -o CpGcount.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calculatecount.c -o calculatecount.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calculatecount1.c -o calculatecount1.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calculatecountneg.c -o calculatecountneg.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pmultinom.c -o pmultinom.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pvalueclassify.c -o pvalueclassify.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o gcc -shared -s -static-libgcc -o methylMnM.dll tmp.def CpGcount.o calculatecount.o calculatecount1.o calculatecountneg.o pmultinom.o pvalueclassify.o register.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-methylMnM/00new/methylMnM/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (methylMnM)
methylMnM.Rcheck/methylMnM-Ex.timings
name | user | system | elapsed | |
CNVnormal | 0.00 | 0.00 | 0.01 | |
MnM.qvalue | 0.06 | 0.00 | 0.08 | |
MnM.selectDMR | 0.02 | 0.00 | 0.01 | |
MnM.test | 0.01 | 0.00 | 0.03 | |
calcFactornew | 0 | 0 | 0 | |
calculatecount | 0 | 0 | 0 | |
calculatecount1 | 0.00 | 0.01 | 0.02 | |
calculatecountneg | 0 | 0 | 0 | |
countMREbin | 0.74 | 0.07 | 0.79 | |
countMREcpgbin | 1.04 | 0.03 | 1.08 | |
countMeDIPbin | 1.05 | 0.01 | 1.07 | |
countcpgbin | 0.75 | 0.08 | 0.84 | |
cpgcount | 0 | 0 | 0 | |
normpdf | 0 | 0 | 0 | |
normpdf1 | 0 | 0 | 0 | |
pmultinom | 0.36 | 0.00 | 0.36 | |
qvalue.rank | 0 | 0 | 0 | |
removeblacklist | 0.03 | 0.00 | 0.03 | |