Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:36 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the MethylSeekR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/MethylSeekR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1127/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MethylSeekR 1.34.0 (landing page) Lukas Burger
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MethylSeekR |
Version: 1.34.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MethylSeekR_1.34.0.tar.gz |
StartedAt: 2022-04-12 08:11:34 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 08:17:01 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 327.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MethylSeekR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MethylSeekR_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MethylSeekR.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MethylSeekR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MethylSeekR’ version ‘1.34.0’ * 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 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 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 42.095 1.005 52.486 savePMDSegments 26.539 0.860 27.447 plotPMDSegmentation 26.278 0.528 26.811 segmentPMDs 22.567 1.273 23.841 calculateFDRs 7.673 0.133 16.370 plotAlphaDistributionOneChr 5.608 0.099 5.708 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/home/biocbuild/bbs-3.14-bioc/meat/MethylSeekR.Rcheck/00check.log’ for details.
MethylSeekR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MethylSeekR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 | 42.095 | 1.005 | 52.486 | |
calculateFDRs | 7.673 | 0.133 | 16.370 | |
plotAlphaDistributionOneChr | 5.608 | 0.099 | 5.708 | |
plotFinalSegmentation | 1.693 | 0.056 | 1.749 | |
plotPMDSegmentation | 26.278 | 0.528 | 26.811 | |
readMethylome | 0.281 | 0.004 | 0.284 | |
readSNPTable | 0.104 | 0.000 | 0.104 | |
removeSNPs | 0.424 | 0.004 | 0.428 | |
savePMDSegments | 26.539 | 0.860 | 27.447 | |
saveUMRLMRSegments | 1.156 | 0.072 | 1.229 | |
segmentPMDs | 22.567 | 1.273 | 23.841 | |
segmentUMRsLMRs | 1.120 | 0.028 | 1.148 | |