Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-01 12:05 -0400 (Mon, 01 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1252/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylPipe 1.43.1 (landing page) Mattia Furlan
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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: 1.43.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylPipe_1.43.1.tar.gz |
StartedAt: 2025-08-31 21:58:16 -0400 (Sun, 31 Aug 2025) |
EndedAt: 2025-08-31 22:06:55 -0400 (Sun, 31 Aug 2025) |
EllapsedTime: 519.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: methylPipe.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylPipe_1.43.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/methylPipe.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methylPipe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylPipe’ version ‘1.43.1’ * 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 ‘methylPipe’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: BSdata-class.Rd: GRanges GEcollection-class.Rd: RangedSummarizedExperiment, GRanges consolidateDMRs.Rd: GRanges extractBinGRanges.Rd: GRanges findDMR.Rd: GRanges getCpos.Rd: GRanges, DNAString getCposDensity.Rd: GRanges mapBSdata2GRanges.Rd: GRanges meth.call.Rd: GRanges plotMeth.Rd: GRanges, GRangesList process.hmc.Rd: GRanges, coverage, GenomicRanges profileDNAmetBin.Rd: GRanges Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 is not available * 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 '/private/tmp/Rtmp6Vu8g8', resetting Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMeth 25.575 0.956 38.049 findDMR 1.216 1.313 34.036 methstats 0.880 0.168 24.463 findPMDs 0.202 0.107 24.052 * 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/methylPipe.Rcheck/00check.log’ for details.
methylPipe.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylPipe ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘methylPipe’ ... ** this is package ‘methylPipe’ version ‘1.43.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_methylPipe.c -o R_init_methylPipe.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c binning.c -o binning.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o methylPipe.so R_init_methylPipe.o binning.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-methylPipe/00new/methylPipe/libs ** 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 ** 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 (methylPipe)
methylPipe.Rcheck/methylPipe-Ex.timings
name | user | system | elapsed | |
BSdata-class | 0.250 | 0.012 | 0.264 | |
BSdataSet-class | 0.177 | 0.010 | 0.188 | |
BSprepare | 0.000 | 0.000 | 0.001 | |
GEcollection-class | 2.848 | 0.073 | 2.940 | |
GElist-class | 0.034 | 0.001 | 0.036 | |
chiCombP | 0 | 0 | 0 | |
consolidateDMRs | 0.216 | 0.003 | 0.221 | |
extractBinGRanges | 0.019 | 0.001 | 0.021 | |
findDMR | 1.216 | 1.313 | 34.036 | |
findPMDs | 0.202 | 0.107 | 24.052 | |
getCpos | 0.117 | 0.013 | 0.131 | |
getCposDensity | 0.117 | 0.011 | 0.128 | |
mCsmoothing | 0.374 | 0.024 | 0.400 | |
mapBSdata2GRanges | 1.117 | 0.014 | 1.136 | |
methstats | 0.880 | 0.168 | 24.463 | |
plotMeth | 25.575 | 0.956 | 38.049 | |
pool.reads | 0.001 | 0.001 | 0.000 | |
process.hmc | 0 | 0 | 0 | |
profileDNAmetBin | 1.369 | 0.065 | 1.441 | |