Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1219/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylPipe 1.39.0 (landing page) Mattia Furlan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the methylPipe package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylPipe.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: methylPipe |
Version: 1.39.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylPipe.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methylPipe_1.39.0.tar.gz |
StartedAt: 2024-08-21 02:34:11 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 02:42:59 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 527.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: methylPipe.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylPipe.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methylPipe_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/methylPipe.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 'methylPipe/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'methylPipe' version '1.39.0' * 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 'methylPipe' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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 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 whether startup messages can be suppressed ... 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 ... NOTE findPMDs,BSdata : PMDchr: no visible global function definition for 'segmentPMDs' show,BSdata: no visible global function definition for 'organism' show,BSdataSet: no visible global function definition for 'organism' Undefined global functions or variables: organism segmentPMDs * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'BSdataSet,ANY,ANY,ANY' generic '[' and siglist 'GElist,ANY,ANY,ANY' generic '[[<-' and siglist 'BSdataSet,ANY,ANY,ANY' generic '[[<-' and siglist 'GElist,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 'F:/biocbuild/bbs-3.20-bioc/R/library/methylPipe/libs/x64/methylPipe.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 ... WARNING Found the following significant warnings: Warning: working directory was changed to 'F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpWOdxPN', resetting Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMeth 24.15 0.96 29.88 findDMR 0.90 2.08 34.26 methstats 0.85 0.23 24.22 findPMDs 0.20 0.12 23.41 * 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: 2 WARNINGs, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/methylPipe.Rcheck/00check.log' for details.
methylPipe.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL methylPipe ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'methylPipe' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/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 R_init_methylPipe.c -o R_init_methylPipe.o gcc -I"F:/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 binning.c -o binning.o gcc -shared -s -static-libgcc -o methylPipe.dll tmp.def R_init_methylPipe.o binning.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-methylPipe/00new/methylPipe/libs/x64 ** R ** exec ** 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 (methylPipe)
methylPipe.Rcheck/methylPipe-Ex.timings
name | user | system | elapsed | |
BSdata-class | 0.26 | 0.05 | 0.31 | |
BSdataSet-class | 0.20 | 0.00 | 0.22 | |
BSprepare | 0 | 0 | 0 | |
GEcollection-class | 2.81 | 0.15 | 2.99 | |
GElist-class | 0.03 | 0.02 | 0.04 | |
chiCombP | 0 | 0 | 0 | |
consolidateDMRs | 0.25 | 0.00 | 0.25 | |
extractBinGRanges | 0.03 | 0.00 | 0.04 | |
findDMR | 0.90 | 2.08 | 34.26 | |
findPMDs | 0.20 | 0.12 | 23.41 | |
getCpos | 0.13 | 0.02 | 0.14 | |
getCposDensity | 0.06 | 0.08 | 0.14 | |
mCsmoothing | 0.31 | 0.03 | 0.35 | |
mapBSdata2GRanges | 1.18 | 0.01 | 1.23 | |
methstats | 0.85 | 0.23 | 24.22 | |
plotMeth | 24.15 | 0.96 | 29.88 | |
pool.reads | 0 | 0 | 0 | |
process.hmc | 0 | 0 | 0 | |
profileDNAmetBin | 1.47 | 0.11 | 1.58 | |