Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-27 12:34 -0400 (Fri, 27 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4451 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
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 1128/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MAGeCKFlute 2.9.0 (landing page) Wubing Zhang
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 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 | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MAGeCKFlute |
Version: 2.9.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MAGeCKFlute_2.9.0.tar.gz |
StartedAt: 2024-09-27 07:29:23 -0000 (Fri, 27 Sep 2024) |
EndedAt: 2024-09-27 07:34:13 -0000 (Fri, 27 Sep 2024) |
EllapsedTime: 289.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MAGeCKFlute.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MAGeCKFlute_2.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MAGeCKFlute.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MAGeCKFlute/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MAGeCKFlute’ version ‘2.9.0’ * 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 loading without being on the library search path ... 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 4.805 0.412 5.225 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/MAGeCKFlute.Rcheck/00check.log’ for details.
MAGeCKFlute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MAGeCKFlute ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 | 0.248 | 0.008 | 0.256 | |
BatchRemove | 4.296 | 0.280 | 4.585 | |
ConsistencyView | 1.184 | 0.060 | 1.247 | |
CutoffCalling | 0.004 | 0.000 | 0.004 | |
DensityDiffView | 1.068 | 0.020 | 1.091 | |
DensityView | 1.242 | 0.024 | 1.268 | |
EnrichAnalyzer | 0.013 | 0.000 | 0.015 | |
EnrichedFilter | 0.011 | 0.000 | 0.011 | |
EnrichedGeneView | 0.011 | 0.000 | 0.011 | |
EnrichedView | 0.011 | 0.000 | 0.011 | |
FluteMLE | 0.001 | 0.000 | 0.001 | |
FluteRRA | 0.002 | 0.000 | 0.002 | |
HeatmapView | 0.501 | 0.003 | 0.505 | |
IdentBarView | 0.191 | 0.020 | 0.212 | |
IncorporateDepmap | 0.262 | 0.008 | 0.272 | |
MAView | 4.805 | 0.412 | 5.225 | |
MapRatesView | 0.440 | 0.003 | 0.444 | |
NormalizeBeta | 0.927 | 0.020 | 0.948 | |
OmitCommonEssential | 0 | 0 | 0 | |
RankView | 0.923 | 0.020 | 0.945 | |
ReadBeta | 0.510 | 0.004 | 0.515 | |
ReadRRA | 0.242 | 0.004 | 0.247 | |
ReadsgRRA | 0.017 | 0.000 | 0.018 | |
ResembleDepmap | 0.249 | 0.000 | 0.250 | |
ScatterView | 3.593 | 0.047 | 3.652 | |
Selector | 0.492 | 0.012 | 0.505 | |
SquareView | 1.459 | 0.080 | 1.542 | |
TransGeneID | 1.888 | 0.012 | 1.908 | |
ViolinView | 1.639 | 0.012 | 1.654 | |
VolcanoView | 2.706 | 0.072 | 2.784 | |
arrangePathview | 0.446 | 0.008 | 0.455 | |
enrich.GSE | 0.01 | 0.00 | 0.01 | |
enrich.HGT | 3.075 | 0.076 | 3.158 | |
enrich.ORT | 4.547 | 0.032 | 4.588 | |
getCols | 0.007 | 0.000 | 0.008 | |
getGeneAnn | 0.000 | 0.000 | 0.001 | |
getOrg | 0.001 | 0.000 | 0.001 | |
getOrtAnn | 0 | 0 | 0 | |
gsGetter | 0.258 | 0.004 | 0.263 | |
hclustView | 0.371 | 0.004 | 0.376 | |
loadDepmap | 0 | 0 | 0 | |
normalize.loess | 1.009 | 0.000 | 1.011 | |
sgRankView | 0.223 | 0.004 | 0.227 | |
writeGMT | 0.124 | 0.000 | 0.125 | |