Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-21 17:41 -0400 (Fri, 21 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" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4506 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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: 2024-06-20 06:39:19 -0400 (Thu, 20 Jun 2024) |
EndedAt: 2024-06-20 06:48:32 -0400 (Thu, 20 Jun 2024) |
EllapsedTime: 552.3 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 22.226 0.533 26.519 enrich.ORT 7.361 0.122 9.020 ScatterView 5.410 0.169 6.486 BatchRemove 5.179 0.202 6.471 * 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 | 0.479 | 0.032 | 0.606 | |
BatchRemove | 5.179 | 0.202 | 6.471 | |
ConsistencyView | 1.731 | 0.099 | 2.172 | |
CutoffCalling | 0.005 | 0.000 | 0.007 | |
DensityDiffView | 1.851 | 0.051 | 2.192 | |
DensityView | 1.899 | 0.088 | 2.312 | |
EnrichAnalyzer | 0.019 | 0.003 | 0.029 | |
EnrichedFilter | 0.018 | 0.001 | 0.022 | |
EnrichedGeneView | 0.017 | 0.002 | 0.022 | |
EnrichedView | 0.018 | 0.001 | 0.021 | |
FluteMLE | 0.002 | 0.001 | 0.003 | |
FluteRRA | 0.003 | 0.002 | 0.005 | |
HeatmapView | 0.630 | 0.020 | 0.745 | |
IdentBarView | 0.322 | 0.006 | 0.355 | |
IncorporateDepmap | 0.388 | 0.017 | 0.463 | |
MAView | 22.226 | 0.533 | 26.519 | |
MapRatesView | 0.851 | 0.016 | 1.009 | |
NormalizeBeta | 1.312 | 0.035 | 1.585 | |
OmitCommonEssential | 0.000 | 0.001 | 0.001 | |
RankView | 1.342 | 0.071 | 1.634 | |
ReadBeta | 0.571 | 0.013 | 0.664 | |
ReadRRA | 0.379 | 0.014 | 0.454 | |
ReadsgRRA | 0.024 | 0.004 | 0.034 | |
ResembleDepmap | 0.312 | 0.007 | 0.363 | |
ScatterView | 5.410 | 0.169 | 6.486 | |
Selector | 1.102 | 0.028 | 1.324 | |
SquareView | 1.996 | 0.080 | 2.381 | |
TransGeneID | 3.830 | 0.053 | 4.442 | |
ViolinView | 2.390 | 0.073 | 2.866 | |
VolcanoView | 2.549 | 0.090 | 3.051 | |
arrangePathview | 0.520 | 0.012 | 0.592 | |
enrich.GSE | 0.017 | 0.002 | 0.022 | |
enrich.HGT | 3.432 | 0.099 | 4.133 | |
enrich.ORT | 7.361 | 0.122 | 9.020 | |
getCols | 0.009 | 0.000 | 0.013 | |
getGeneAnn | 0.000 | 0.001 | 0.001 | |
getOrg | 0.002 | 0.001 | 0.002 | |
getOrtAnn | 0.000 | 0.000 | 0.003 | |
gsGetter | 0.599 | 0.014 | 0.731 | |
hclustView | 0.750 | 0.027 | 0.921 | |
loadDepmap | 0.000 | 0.000 | 0.001 | |
normalize.loess | 2.303 | 0.057 | 2.946 | |
sgRankView | 0.389 | 0.004 | 0.446 | |
writeGMT | 0.043 | 0.002 | 0.055 | |