Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:37 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the MAGeCKFlute package: - 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: 2024-05-06 22:39:39 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 22:41:10 -0400 (Mon, 06 May 2024) |
EllapsedTime: 91.0 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-mac-arm64/meat/MAGeCKFlute.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * 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 enrich.HGT: no visible global function definition for ‘new’ 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’ 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 * 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-mac-arm64/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-arm64/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 | 0.056 | 0.001 | 0.058 | |
BatchRemove | 1.451 | 0.028 | 1.480 | |
ConsistencyView | 0.308 | 0.016 | 0.326 | |
CutoffCalling | 0.001 | 0.000 | 0.002 | |
DensityDiffView | 0.403 | 0.005 | 0.409 | |
DensityView | 0.251 | 0.011 | 0.261 | |
EnrichAnalyzer | 0.006 | 0.000 | 0.007 | |
EnrichedFilter | 0.003 | 0.000 | 0.003 | |
EnrichedGeneView | 0.004 | 0.000 | 0.004 | |
EnrichedView | 0.004 | 0.001 | 0.004 | |
FluteMLE | 0.001 | 0.000 | 0.000 | |
FluteRRA | 0.000 | 0.000 | 0.001 | |
HeatmapView | 0.119 | 0.006 | 0.126 | |
IdentBarView | 0.039 | 0.001 | 0.039 | |
IncorporateDepmap | 0.066 | 0.001 | 0.068 | |
MAView | 3.586 | 0.077 | 3.665 | |
MapRatesView | 0.178 | 0.001 | 0.179 | |
NormalizeBeta | 0.440 | 0.009 | 0.450 | |
OmitCommonEssential | 0 | 0 | 0 | |
RankView | 0.251 | 0.012 | 0.265 | |
ReadBeta | 0.102 | 0.003 | 0.104 | |
ReadRRA | 0.067 | 0.002 | 0.070 | |
ReadsgRRA | 0.006 | 0.001 | 0.006 | |
ResembleDepmap | 0.060 | 0.002 | 0.063 | |
ScatterView | 1.590 | 0.031 | 1.621 | |
Selector | 0.281 | 0.003 | 0.284 | |
SquareView | 0.327 | 0.009 | 0.335 | |
TransGeneID | 0.746 | 0.013 | 0.760 | |
ViolinView | 0.580 | 0.019 | 0.598 | |
VolcanoView | 1.168 | 0.024 | 1.192 | |
arrangePathview | 0.110 | 0.004 | 0.114 | |
enrich.GSE | 0.005 | 0.000 | 0.005 | |
enrich.HGT | 0.764 | 0.019 | 0.782 | |
enrich.ORT | 1.876 | 0.067 | 1.944 | |
getCols | 0.003 | 0.000 | 0.003 | |
getGeneAnn | 0 | 0 | 0 | |
getOrg | 0 | 0 | 0 | |
getOrtAnn | 0 | 0 | 0 | |
gsGetter | 0.086 | 0.004 | 0.090 | |
hclustView | 0.231 | 0.004 | 0.236 | |
loadDepmap | 0 | 0 | 0 | |
normalize.loess | 0.492 | 0.013 | 0.504 | |
sgRankView | 0.051 | 0.001 | 0.051 | |
writeGMT | 0.014 | 0.001 | 0.015 | |