Wubing Zhang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MAGeCKFlute |
| Branch: RELEASE_3_9 |
| Last Commit: 73044ca |
| Last Changed Date: 2019-08-08 00:05:57 -0400 (Thu, 08 Aug 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:12:53 -0400 (Wed, 16 Oct 2019).
| Package 906/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAGeCKFlute 1.4.3 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 | |
| Package: MAGeCKFlute |
| Version: 1.4.3 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MAGeCKFlute_1.4.3.tar.gz |
| StartedAt: 2019-10-16 02:49:52 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:56:08 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 376.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAGeCKFlute.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MAGeCKFlute_1.4.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MAGeCKFlute.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.3’
* 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 16.3Mb
sub-directories of 1Mb or more:
data 5.3Mb
doc 1.2Mb
extdata 9.5Mb
* 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
File ‘MAGeCKFlute/R/zzz.R’:
.onLoad calls:
packageStartupMessage(paste(strwrap(disclaimer, 80), collapse = "\n"))
See section ‘Good practice’ in '?.onAttach'.
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’
EnrichedFilter: no visible binding for global variable ‘max_value’
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 ‘Description’
EnrichedView: no visible binding for global variable ‘size’
FluteMLE: no visible binding for global variable ‘Zuber_Essential’
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 ‘x’
SquareView: no visible binding for global variable ‘y’
SquareView: no visible binding for global variable ‘group’
SquareView: no visible binding for global variable ‘Gene’
ViolinView: no visible binding for global variable ‘variable’
ViolinView: no visible binding for global variable ‘value’
VolcanoView: no visible binding for global variable ‘group’
VolcanoView: no visible binding for global variable ‘color’
sgRankView: no visible global function definition for ‘.’
sgRankView: no visible binding for global variable ‘LFC’
sgRankView: no visible binding for global variable ‘Gene’
sgRankView: no visible binding for global variable ‘x’
sgRankView: no visible binding for global variable ‘y’
sgRankView: no visible binding for global variable ‘value’
sgRankView: no visible binding for global variable ‘id’
sgRankView: no visible binding for global variable ‘yend’
Undefined global functions or variables:
. ..density.. Control Description Diff Gene GeneNum GeneScore LFC PC1
PC2 Rank Size Term Treatment Zuber_Essential category color count
group id keggConv max_value parseKGML2Graph2 percent pos r rn.list
shape size value variable x y yend
* 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
enrich.ORT 22.744 0.004 22.748
EnrichAnalyzer 20.045 0.148 20.320
enrich.HGT 16.920 0.020 16.942
arrangePathview 15.183 0.212 17.424
EnrichedGeneView 15.010 0.020 14.792
EnrichedFilter 14.787 0.056 14.478
gsGetter 8.383 0.036 8.421
TransGeneID 7.115 0.000 7.121
getOrg 7.087 0.003 7.091
MAView 5.331 0.024 5.356
VolcanoView 5.197 0.004 5.202
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/MAGeCKFlute.Rcheck/00check.log’
for details.
MAGeCKFlute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MAGeCKFlute ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 | 1.557 | 0.284 | 1.870 | |
| CellCycleView | 1.067 | 0.011 | 1.085 | |
| CutoffCalling | 0.001 | 0.004 | 0.005 | |
| DensityDiffView | 1.239 | 0.016 | 1.255 | |
| DensityView | 0.615 | 0.001 | 0.615 | |
| EnrichAB | 0.043 | 0.000 | 0.042 | |
| EnrichAnalyzer | 20.045 | 0.148 | 20.320 | |
| EnrichSquare | 0.112 | 0.008 | 0.120 | |
| EnrichedFilter | 14.787 | 0.056 | 14.478 | |
| EnrichedGeneView | 15.010 | 0.020 | 14.792 | |
| EnrichedView | 0 | 0 | 0 | |
| FluteMLE | 0.001 | 0.000 | 0.001 | |
| FluteRRA | 0.001 | 0.000 | 0.001 | |
| HeatmapView | 0.063 | 0.000 | 0.063 | |
| IdentBarView | 0.230 | 0.004 | 0.235 | |
| KeggPathwayView | 0.022 | 0.000 | 0.022 | |
| MAView | 5.331 | 0.024 | 5.356 | |
| MapRatesView | 0.387 | 0.000 | 0.386 | |
| NormalizeBeta | 0.224 | 0.000 | 0.224 | |
| RankView | 1.093 | 0.008 | 1.101 | |
| ReadBeta | 0.018 | 0.004 | 0.022 | |
| ReadRRA | 0.245 | 0.000 | 0.245 | |
| ReadsgRRA | 0.184 | 0.000 | 0.183 | |
| ScatterView | 0.541 | 0.000 | 0.541 | |
| Selector | 0.222 | 0.004 | 0.227 | |
| SquareView | 1.083 | 0.012 | 1.094 | |
| TransGeneID | 7.115 | 0.000 | 7.121 | |
| ViolinView | 1.740 | 0.008 | 1.748 | |
| VolcanoView | 5.197 | 0.004 | 5.202 | |
| arrangePathview | 15.183 | 0.212 | 17.424 | |
| countsummary | 0.002 | 0.004 | 0.006 | |
| enrich.GSE | 0.013 | 0.000 | 0.014 | |
| enrich.HGT | 16.920 | 0.020 | 16.942 | |
| enrich.ORT | 22.744 | 0.004 | 22.748 | |
| getOrg | 7.087 | 0.003 | 7.091 | |
| gsGetter | 8.383 | 0.036 | 8.421 | |
| mle.gene_summary | 0.035 | 0.000 | 0.036 | |
| normalize.loess | 0.411 | 0.000 | 0.411 | |
| rra.gene_summary | 0.026 | 0.004 | 0.029 | |
| rra.sgrna_summary | 0.489 | 0.000 | 0.490 | |
| sgRankView | 1.116 | 0.000 | 0.759 | |