Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1147/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MAGeCKFlute 2.8.0 (landing page) Wubing Zhang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the MAGeCKFlute package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAGeCKFlute.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: MAGeCKFlute |
Version: 2.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAGeCKFlute_2.8.0.tar.gz |
StartedAt: 2024-06-24 06:50:31 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 06:59:43 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 551.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MAGeCKFlute.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAGeCKFlute_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MAGeCKFlute.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MAGeCKFlute/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MAGeCKFlute’ version ‘2.8.0’ * package encoding: UTF-8 * 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 ‘MAGeCKFlute’ can be installed ... OK * checking installed package size ... NOTE installed size is 20.7Mb sub-directories of 1Mb or more: extdata 20.3Mb * 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 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 EnrichedFilter: no visible global function definition for ‘is’ EnrichedGeneView: no visible global function definition for ‘is’ EnrichedView: no visible global function definition for ‘is’ EnrichedView: no visible global function definition for ‘slot’ enrich.HGT: no visible global function definition for ‘new’ Undefined global functions or variables: is new slot Consider adding importFrom("methods", "is", "new", "slot") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) FluteMLE.Rd:87: Lost braces; missing escapes or markup? 87 | \item {QC}: {Quality control} | ^ checkRd: (-1) FluteMLE.Rd:88: Lost braces; missing escapes or markup? 88 | \item {Selection}: {Positive selection and negative selection.} | ^ checkRd: (-1) FluteMLE.Rd:89: Lost braces; missing escapes or markup? 89 | \item {Enrichment}: {Enrichment analysis for positive and negative selection genes.} | ^ checkRd: (-1) FluteMLE.Rd:90: Lost braces; missing escapes or markup? 90 | \item {PathwayView}: {Pathway view for top enriched pathways.} | ^ checkRd: (-1) getOrg.Rd:18: Lost braces 18 | \code{pkg}{annotation package name} | ^ * 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 MAView 22.092 0.478 25.923 enrich.ORT 7.383 0.118 8.405 ScatterView 5.376 0.174 6.122 BatchRemove 5.220 0.189 6.431 * 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-3.19-bioc/meat/MAGeCKFlute.Rcheck/00check.log’ for details.
MAGeCKFlute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MAGeCKFlute ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MAGeCKFlute’ ... ** 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 (MAGeCKFlute)
MAGeCKFlute.Rcheck/MAGeCKFlute-Ex.timings
name | user | system | elapsed | |
BarView | 0.471 | 0.029 | 0.581 | |
BatchRemove | 5.220 | 0.189 | 6.431 | |
ConsistencyView | 1.670 | 0.093 | 2.024 | |
CutoffCalling | 0.006 | 0.001 | 0.007 | |
DensityDiffView | 1.889 | 0.050 | 2.242 | |
DensityView | 1.912 | 0.084 | 2.318 | |
EnrichAnalyzer | 0.019 | 0.002 | 0.027 | |
EnrichedFilter | 0.016 | 0.001 | 0.022 | |
EnrichedGeneView | 0.017 | 0.001 | 0.020 | |
EnrichedView | 0.017 | 0.002 | 0.022 | |
FluteMLE | 0.001 | 0.000 | 0.002 | |
FluteRRA | 0.004 | 0.002 | 0.005 | |
HeatmapView | 0.615 | 0.015 | 0.722 | |
IdentBarView | 0.325 | 0.004 | 0.417 | |
IncorporateDepmap | 0.383 | 0.011 | 0.458 | |
MAView | 22.092 | 0.478 | 25.923 | |
MapRatesView | 0.848 | 0.011 | 0.979 | |
NormalizeBeta | 1.320 | 0.031 | 1.526 | |
OmitCommonEssential | 0.000 | 0.001 | 0.004 | |
RankView | 1.282 | 0.070 | 1.513 | |
ReadBeta | 0.550 | 0.012 | 0.605 | |
ReadRRA | 0.384 | 0.010 | 0.440 | |
ReadsgRRA | 0.022 | 0.002 | 0.028 | |
ResembleDepmap | 0.317 | 0.006 | 0.366 | |
ScatterView | 5.376 | 0.174 | 6.122 | |
Selector | 1.093 | 0.023 | 1.264 | |
SquareView | 2.023 | 0.078 | 2.377 | |
TransGeneID | 3.802 | 0.060 | 4.506 | |
ViolinView | 2.370 | 0.067 | 2.810 | |
VolcanoView | 2.505 | 0.086 | 2.930 | |
arrangePathview | 0.538 | 0.013 | 0.650 | |
enrich.GSE | 0.017 | 0.001 | 0.020 | |
enrich.HGT | 3.465 | 0.097 | 4.022 | |
enrich.ORT | 7.383 | 0.118 | 8.405 | |
getCols | 0.010 | 0.001 | 0.013 | |
getGeneAnn | 0.000 | 0.000 | 0.001 | |
getOrg | 0.002 | 0.000 | 0.002 | |
getOrtAnn | 0.000 | 0.001 | 0.001 | |
gsGetter | 0.563 | 0.011 | 0.644 | |
hclustView | 0.743 | 0.033 | 0.881 | |
loadDepmap | 0.001 | 0.000 | 0.000 | |
normalize.loess | 2.322 | 0.054 | 2.737 | |
sgRankView | 0.401 | 0.004 | 0.481 | |
writeGMT | 0.046 | 0.003 | 0.059 | |