Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:07 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1231/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylPipe 1.36.0 (landing page) Mattia Furlan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.36.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings methylPipe_1.36.0.tar.gz |
StartedAt: 2024-04-16 00:46:45 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 00:57:52 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 666.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: methylPipe.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings methylPipe_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/methylPipe.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘methylPipe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylPipe’ version ‘1.36.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘methylPipe’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 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 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: working directory was changed to '/tmp/RtmpKCahlY', resetting Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMeth 23.454 1.839 32.471 findDMR 0.795 0.837 32.559 methstats 0.826 0.188 21.870 findPMDs 0.144 0.079 21.313 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘methylPipe.rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/methylPipe.Rcheck/00check.log’ for details.
methylPipe.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL methylPipe ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘methylPipe’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_methylPipe.c -o R_init_methylPipe.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c binning.c -o binning.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o methylPipe.so R_init_methylPipe.o binning.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.18-bioc/R/site-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 | 0.197 | 0.013 | 0.210 | |
BSdataSet-class | 0.144 | 0.000 | 0.144 | |
BSprepare | 0 | 0 | 0 | |
GEcollection-class | 2.979 | 0.236 | 3.215 | |
GElist-class | 0.031 | 0.000 | 0.030 | |
chiCombP | 0.000 | 0.000 | 0.001 | |
consolidateDMRs | 0.167 | 0.004 | 0.170 | |
extractBinGRanges | 0.018 | 0.000 | 0.018 | |
findDMR | 0.795 | 0.837 | 32.559 | |
findPMDs | 0.144 | 0.079 | 21.313 | |
getCpos | 0.109 | 0.004 | 0.112 | |
getCposDensity | 0.086 | 0.022 | 0.108 | |
mCsmoothing | 0.288 | 0.046 | 0.334 | |
mapBSdata2GRanges | 0.940 | 0.076 | 1.016 | |
methstats | 0.826 | 0.188 | 21.870 | |
plotMeth | 23.454 | 1.839 | 32.471 | |
pool.reads | 0 | 0 | 0 | |
process.hmc | 0 | 0 | 0 | |
profileDNAmetBin | 1.306 | 0.052 | 1.358 | |