Back to Build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-07 15:40 -0400 (Sat, 07 Sep 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" | 4711 |
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 1223/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MethylSeekR 1.45.0 (landing page) Lukas Burger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
To the developers/maintainers of the MethylSeekR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethylSeekR.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: MethylSeekR |
Version: 1.45.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MethylSeekR_1.45.0.tar.gz |
StartedAt: 2024-09-06 23:17:51 -0400 (Fri, 06 Sep 2024) |
EndedAt: 2024-09-06 23:24:59 -0400 (Fri, 06 Sep 2024) |
EllapsedTime: 427.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MethylSeekR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MethylSeekR_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MethylSeekR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * 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 ‘MethylSeekR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MethylSeekR’ version ‘1.45.0’ * 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 ‘MethylSeekR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘parallel’ A package should be listed in only one of these fields. * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘geneplotter’ All declared Imports should be used. Package in Depends field not imported from: ‘rtracklayer’ 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 PMDviterbiSegmentation : <anonymous>: no visible global function definition for ‘values’ PMDviterbiSegmentation : <anonymous>: no visible global function definition for ‘predict’ PMDviterbiSegmentation : <anonymous>: no visible global function definition for ‘Rle’ PMDviterbiSegmentation : <anonymous>: no visible global function definition for ‘runValue’ calculateAlphaDistr : <anonymous>: no visible global function definition for ‘Rle’ calculateFDRs: no visible global function definition for ‘values’ calculateFDRs: no visible global function definition for ‘queryHits’ calculateFDRs: no visible global function definition for ‘values<-’ calculateFDRs : <anonymous>: no visible global function definition for ‘Rle’ calculateFDRs : <anonymous>: no visible global function definition for ‘values’ calculateFDRs : <anonymous>: no visible global function definition for ‘runValue’ createGRangesObjectPMDSegmentation : <anonymous>: no visible global function definition for ‘Rle’ createGRangesObjectPMDSegmentation : <anonymous>: no visible global function definition for ‘nrun’ createGRangesObjectPMDSegmentation : <anonymous>: no visible global function definition for ‘runValue’ plotAlphaDistributionOneChr: no visible global function definition for ‘values’ plotFinalSegmentation: no visible global function definition for ‘values’ plotFinalSegmentation: no visible global function definition for ‘Rle’ plotPMDSegmentation: no visible global function definition for ‘values’ readMethylome: no visible global function definition for ‘values’ removeSNPs: no visible global function definition for ‘queryHits’ savePMDSegments: no visible global function definition for ‘values’ saveUMRLMRSegments: no visible global function definition for ‘values’ segmentUMRsLMRs: no visible global function definition for ‘values’ segmentUMRsLMRs : <anonymous>: no visible global function definition for ‘Rle’ segmentUMRsLMRs : <anonymous>: no visible global function definition for ‘values’ segmentUMRsLMRs : <anonymous>: no visible global function definition for ‘runValue’ segmentUMRsLMRs: no visible global function definition for ‘queryHits’ segmentUMRsLMRs: no visible global function definition for ‘subjectHits’ segmentUMRsLMRs: no visible global function definition for ‘Rle’ segmentUMRsLMRs: no visible global function definition for ‘values<-’ segmentUMRsLMRs: no visible global function definition for ‘DataFrame’ segmentUMRsLMRs: no visible global function definition for ‘colorRampPalette’ trainPMDHMM: no visible global function definition for ‘values’ Undefined global functions or variables: DataFrame Rle colorRampPalette nrun predict queryHits runValue subjectHits values values<- Consider adding importFrom("grDevices", "colorRampPalette") importFrom("stats", "predict") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MethylSeekR-package 40.034 1.177 55.361 savePMDSegments 24.265 0.223 24.489 plotPMDSegmentation 23.830 0.199 24.030 segmentPMDs 23.250 0.128 23.379 calculateFDRs 7.060 0.788 17.728 plotAlphaDistributionOneChr 5.276 1.040 6.317 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/MethylSeekR.Rcheck/00check.log’ for details.
MethylSeekR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MethylSeekR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘MethylSeekR’ ... ** using staged installation ** 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 (MethylSeekR)
MethylSeekR.Rcheck/MethylSeekR-Ex.timings
name | user | system | elapsed | |
MethylSeekR-package | 40.034 | 1.177 | 55.361 | |
calculateFDRs | 7.060 | 0.788 | 17.728 | |
plotAlphaDistributionOneChr | 5.276 | 1.040 | 6.317 | |
plotFinalSegmentation | 1.736 | 0.084 | 1.820 | |
plotPMDSegmentation | 23.830 | 0.199 | 24.030 | |
readMethylome | 0.304 | 0.004 | 0.308 | |
readSNPTable | 0.092 | 0.009 | 0.100 | |
removeSNPs | 0.420 | 0.000 | 0.419 | |
savePMDSegments | 24.265 | 0.223 | 24.489 | |
saveUMRLMRSegments | 1.157 | 0.012 | 1.169 | |
segmentPMDs | 23.250 | 0.128 | 23.379 | |
segmentUMRsLMRs | 1.105 | 0.032 | 1.136 | |