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 13:19:34 -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 03:11:30 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:24:22 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 772.0 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) (2019-03-18 r76245)
* 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 43.094 5.175 48.274
MAView 44.630 0.442 45.078
arrangePathview 30.643 1.205 33.812
enrich.ORT 26.241 0.620 26.861
EnrichedGeneView 22.738 1.161 23.028
RankView 17.513 0.318 17.992
CellCycleView 15.444 0.450 15.897
ScatterView 15.361 0.326 15.746
enrich.HGT 15.100 0.571 15.662
SquareView 14.586 0.393 15.035
enrichment_analysis 14.498 0.466 14.965
ViolinView 14.504 0.375 14.989
VolcanoView 14.362 0.311 14.692
NormalizeBeta 13.739 0.247 13.997
ReadBeta 13.408 0.274 13.697
DensityView 13.321 0.300 13.625
EnrichAB 13.196 0.209 13.406
DensityDiffView 13.116 0.279 13.396
ReadRRA 12.766 0.217 13.039
normalize.loess 12.650 0.184 12.834
HeatmapView 11.890 0.282 12.172
TransGeneID 11.788 0.257 24.671
EnrichSquare 11.569 0.215 11.784
getOrg 11.407 0.157 11.565
* 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’ ... ** using staged installation ** 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 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 | |
| BatchRemove | 1.218 | 0.075 | 1.296 | |
| CellCycleView | 15.444 | 0.450 | 15.897 | |
| CorrView | 0.832 | 0.017 | 0.851 | |
| CutoffCalling | 0.003 | 0.000 | 0.004 | |
| DensityDiffView | 13.116 | 0.279 | 13.396 | |
| DensityView | 13.321 | 0.300 | 13.625 | |
| EnrichAB | 13.196 | 0.209 | 13.406 | |
| EnrichSquare | 11.569 | 0.215 | 11.784 | |
| EnrichedGSEView | 0.001 | 0.000 | 0.001 | |
| EnrichedGeneView | 22.738 | 1.161 | 23.028 | |
| EnrichedView | 43.094 | 5.175 | 48.274 | |
| FluteMLE | 0.002 | 0.002 | 0.004 | |
| FluteRRA | 0.001 | 0.002 | 0.004 | |
| HeatmapView | 11.890 | 0.282 | 12.172 | |
| IdentBarView | 0.290 | 0.005 | 0.295 | |
| KeggPathwayView | 0.025 | 0.010 | 0.038 | |
| MAView | 44.630 | 0.442 | 45.078 | |
| MapRatesView | 0.631 | 0.010 | 0.642 | |
| NormalizeBeta | 13.739 | 0.247 | 13.997 | |
| RankView | 17.513 | 0.318 | 17.992 | |
| ReadBeta | 13.408 | 0.274 | 13.697 | |
| ReadRRA | 12.766 | 0.217 | 13.039 | |
| ReadsgRRA | 0.529 | 0.053 | 0.582 | |
| ScatterView | 15.361 | 0.326 | 15.746 | |
| Selector | 0.440 | 0.007 | 0.450 | |
| SquareView | 14.586 | 0.393 | 15.035 | |
| TransGeneID | 11.788 | 0.257 | 24.671 | |
| ViolinView | 14.504 | 0.375 | 14.989 | |
| VolcanoView | 14.362 | 0.311 | 14.692 | |
| arrangePathview | 30.643 | 1.205 | 33.812 | |
| countsummary | 0.010 | 0.005 | 0.014 | |
| enrich.GSE | 0.013 | 0.001 | 0.013 | |
| enrich.HGT | 15.100 | 0.571 | 15.662 | |
| enrich.ORT | 26.241 | 0.620 | 26.861 | |
| enrichment_analysis | 14.498 | 0.466 | 14.965 | |
| getOrg | 11.407 | 0.157 | 11.565 | |
| mle.gene_summary | 0.038 | 0.011 | 0.050 | |
| normalize.loess | 12.650 | 0.184 | 12.834 | |
| rra.gene_summary | 0.023 | 0.006 | 0.030 | |
| rra.sgrna_summary | 0.200 | 0.028 | 0.228 | |
| sgRankView | 0.768 | 0.095 | 0.863 | |