Wubing Zhang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MAGeCKFlute |
| Branch: master |
| Last Commit: 96c713f |
| Last Changed Date: 2018-12-09 07:15:06 -0400 (Sun, 09 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:36:14 -0400 (Tue, 09 Apr 2019).
| Package 891/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAGeCKFlute 1.3.1 Wubing Zhang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: MAGeCKFlute |
| Version: 1.3.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAGeCKFlute_1.3.1.tar.gz |
| StartedAt: 2019-04-09 01:55:03 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:05:11 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 607.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAGeCKFlute.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAGeCKFlute_1.3.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MAGeCKFlute.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAGeCKFlute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAGeCKFlute’ version ‘1.3.1’
* 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 11.7Mb
sub-directories of 1Mb or more:
data 5.3Mb
doc 1.5Mb
extdata 4.5Mb
* 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BatchRemove: no visible binding for global variable ‘PC1’
BatchRemove: no visible binding for global variable ‘PC2’
BatchRemove: no visible binding for global variable ‘shape’
CellCycleView: no visible binding for global variable ‘x’
CellCycleView: no visible binding for global variable ‘y’
DensityDiffView: no visible binding for global variable ‘Diff’
DensityDiffView: no visible binding for global variable ‘..density..’
DensityDiffView: no visible binding for global variable ‘r’
DensityView: no visible binding for global variable ‘value’
DensityView: no visible binding for global variable ‘variable’
EnrichedGSEView: no visible binding for global variable ‘NES’
EnrichedGSEView: no visible binding for global variable ‘Name’
EnrichedGSEView: no visible binding for global variable ‘logP’
EnrichedGeneView: no visible binding for global variable ‘Gene’
EnrichedGeneView: no visible binding for global variable ‘Term’
EnrichedGeneView: no visible binding for global variable ‘Size’
EnrichedGeneView: no visible binding for global variable ‘GeneScore’
EnrichedView: no visible binding for global variable ‘logP’
EnrichedView: no visible binding for global variable ‘Name’
EnrichedView: no visible binding for global variable ‘Count’
FluteMLE: no visible binding for global variable ‘Zuber_Essential’
KeggPathwayView: no visible binding for global variable ‘bods’
KeggPathwayView: no visible global function definition for ‘keggConv’
KeggPathwayView: no visible binding for global variable ‘rn.list’
KeggPathwayView: no visible global function definition for
‘parseKGML2Graph2’
MapRatesView: no visible binding for global variable ‘count’
MapRatesView: no visible binding for global variable ‘category’
MapRatesView: no visible binding for global variable ‘pos’
MapRatesView: no visible binding for global variable ‘percent’
NormalizeBeta: no visible binding for global variable ‘Zuber_Essential’
RankView: no visible binding for global variable ‘Rank’
RankView: no visible binding for global variable ‘group’
RankView: no visible binding for global variable ‘Gene’
ScatterView: no visible binding for global variable ‘Control’
ScatterView: no visible binding for global variable ‘Treatment’
ScatterView: no visible binding for global variable ‘group’
Selector: no visible binding for global variable ‘GeneNum’
Selector: no visible binding for global variable ‘x’
Selector: no visible binding for global variable ‘y’
SquareView: no visible binding for global variable ‘Control’
SquareView: no visible binding for global variable ‘Treatment’
SquareView: no visible binding for global variable ‘group’
SquareView: no visible binding for global variable ‘Gene’
TransGeneID: no visible binding for global variable ‘bods’
ViolinView: no visible binding for global variable ‘variable’
ViolinView: no visible binding for global variable ‘value’
VolcanoView: no visible binding for global variable ‘group’
getOrg: no visible binding for global variable ‘bods’
sgRankView: no visible binding for global variable ‘LFC’
sgRankView: no visible binding for global variable ‘Gene’
sgRankView: no visible binding for global variable ‘x_end’
sgRankView: no visible binding for global variable ‘group’
Undefined global functions or variables:
..density.. Control Count Diff Gene GeneNum GeneScore LFC NES Name
PC1 PC2 Rank Size Term Treatment Zuber_Essential bods category count
group keggConv logP parseKGML2Graph2 percent pos r rn.list shape
value variable x x_end y
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EnrichedView 33.380 2.083 35.779
arrangePathview 27.709 0.713 30.516
enrich.ORT 23.478 0.366 24.026
MAView 20.119 0.205 20.482
EnrichedGeneView 16.701 0.885 16.665
RankView 13.993 0.154 14.299
ScatterView 13.065 0.201 13.409
VolcanoView 12.902 0.163 13.204
enrich.HGT 12.557 0.217 12.922
enrichment_analysis 12.532 0.235 12.847
ReadRRA 12.417 0.142 12.699
SquareView 12.118 0.183 12.396
ViolinView 12.078 0.219 12.397
CellCycleView 12.057 0.221 12.373
ReadBeta 12.069 0.154 12.384
DensityDiffView 11.842 0.162 12.099
TransGeneID 11.805 0.144 21.148
DensityView 11.530 0.144 11.765
EnrichSquare 11.040 0.110 11.239
NormalizeBeta 10.667 0.132 10.898
EnrichAB 10.558 0.107 10.742
normalize.loess 10.497 0.118 10.719
HeatmapView 10.405 0.151 10.668
getOrg 9.893 0.085 10.072
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/MAGeCKFlute.Rcheck/00check.log’
for details.
MAGeCKFlute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MAGeCKFlute ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘MAGeCKFlute’ ... ** R ** data *** moving datasets to lazyload DB ** 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 * DONE (MAGeCKFlute)
MAGeCKFlute.Rcheck/MAGeCKFlute-Ex.timings
| name | user | system | elapsed | |
| BatchRemove | 1.051 | 0.041 | 1.100 | |
| CellCycleView | 12.057 | 0.221 | 12.373 | |
| CorrView | 0.726 | 0.008 | 0.738 | |
| CutoffCalling | 0.005 | 0.000 | 0.006 | |
| DensityDiffView | 11.842 | 0.162 | 12.099 | |
| DensityView | 11.530 | 0.144 | 11.765 | |
| EnrichAB | 10.558 | 0.107 | 10.742 | |
| EnrichSquare | 11.040 | 0.110 | 11.239 | |
| EnrichedGSEView | 0 | 0 | 0 | |
| EnrichedGeneView | 16.701 | 0.885 | 16.665 | |
| EnrichedView | 33.380 | 2.083 | 35.779 | |
| FluteMLE | 0.002 | 0.002 | 0.004 | |
| FluteRRA | 0.002 | 0.002 | 0.004 | |
| HeatmapView | 10.405 | 0.151 | 10.668 | |
| IdentBarView | 0.208 | 0.002 | 0.211 | |
| KeggPathwayView | 0.020 | 0.004 | 0.024 | |
| MAView | 20.119 | 0.205 | 20.482 | |
| MapRatesView | 0.552 | 0.013 | 0.572 | |
| NormalizeBeta | 10.667 | 0.132 | 10.898 | |
| RankView | 13.993 | 0.154 | 14.299 | |
| ReadBeta | 12.069 | 0.154 | 12.384 | |
| ReadRRA | 12.417 | 0.142 | 12.699 | |
| ReadsgRRA | 0.234 | 0.021 | 0.256 | |
| ScatterView | 13.065 | 0.201 | 13.409 | |
| Selector | 0.324 | 0.005 | 0.332 | |
| SquareView | 12.118 | 0.183 | 12.396 | |
| TransGeneID | 11.805 | 0.144 | 21.148 | |
| ViolinView | 12.078 | 0.219 | 12.397 | |
| VolcanoView | 12.902 | 0.163 | 13.204 | |
| arrangePathview | 27.709 | 0.713 | 30.516 | |
| countsummary | 0.007 | 0.002 | 0.010 | |
| enrich.GSE | 0.014 | 0.001 | 0.015 | |
| enrich.HGT | 12.557 | 0.217 | 12.922 | |
| enrich.ORT | 23.478 | 0.366 | 24.026 | |
| enrichment_analysis | 12.532 | 0.235 | 12.847 | |
| getOrg | 9.893 | 0.085 | 10.072 | |
| mle.gene_summary | 0.030 | 0.006 | 0.036 | |
| normalize.loess | 10.497 | 0.118 | 10.719 | |
| rra.gene_summary | 0.020 | 0.003 | 0.023 | |
| rra.sgrna_summary | 0.151 | 0.014 | 0.166 | |
| sgRankView | 0.369 | 0.023 | 0.394 | |