Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1235/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MethylSeekR 1.46.0 (landing page) Lukas Burger
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.46.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MethylSeekR_1.46.0.tar.gz |
StartedAt: 2024-11-19 23:55:36 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-20 00:04:37 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 540.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MethylSeekR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MethylSeekR_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MethylSeekR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MethylSeekR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MethylSeekR’ version ‘1.46.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MethylSeekR-package 34.495 2.955 55.826 savePMDSegments 20.653 1.984 22.718 plotPMDSegmentation 20.214 1.701 21.996 segmentPMDs 19.153 1.886 21.101 calculateFDRs 5.097 0.753 15.423 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MethylSeekR.Rcheck/00check.log’ for details.
MethylSeekR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MethylSeekR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 34.495 | 2.955 | 55.826 | |
calculateFDRs | 5.097 | 0.753 | 15.423 | |
plotAlphaDistributionOneChr | 4.150 | 0.379 | 4.544 | |
plotFinalSegmentation | 1.183 | 0.106 | 1.292 | |
plotPMDSegmentation | 20.214 | 1.701 | 21.996 | |
readMethylome | 0.243 | 0.010 | 0.254 | |
readSNPTable | 0.082 | 0.008 | 0.090 | |
removeSNPs | 0.314 | 0.035 | 0.349 | |
savePMDSegments | 20.653 | 1.984 | 22.718 | |
saveUMRLMRSegments | 0.873 | 0.121 | 0.999 | |
segmentPMDs | 19.153 | 1.886 | 21.101 | |
segmentUMRsLMRs | 0.852 | 0.088 | 0.945 | |