Wubing Zhang
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MAGeCKFlute |
| Branch: RELEASE_3_8 |
| Last Commit: 0df39fe |
| Last Changed Date: 2019-02-21 01:04:56 -0400 (Thu, 21 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:28:40 -0400 (Sat, 13 Apr 2019).
| Package 867/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAGeCKFlute 1.2.3 Wubing Zhang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MAGeCKFlute |
| Version: 1.2.3 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGeCKFlute.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.2.3.tar.gz |
| StartedAt: 2019-04-13 03:29:37 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:42:31 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 774.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAGeCKFlute.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGeCKFlute.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.2.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MAGeCKFlute.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MAGeCKFlute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAGeCKFlute' version '1.2.3'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package 'MAGeCKFlute' can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.5Mb
sub-directories of 1Mb or more:
data 5.3Mb
extdata 4.6Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 'Description'
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 'Description'
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'
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 '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 'LFC'
sgRankView: no visible binding for global variable 'yend'
Undefined global functions or variables:
..density.. Control Count Description Diff Gene GeneNum GeneScore LFC
NES PC1 PC2 Rank Size Term Treatment Zuber_Essential bods category
count group id keggConv logP parseKGML2Graph2 percent pos r rn.list
shape 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
arrangePathview 18.50 0.70 20.35
enrich.ORT 13.19 0.00 13.19
MAView 11.97 0.61 12.58
EnrichedView 11.64 0.14 11.78
RankView 10.63 0.05 10.67
enrichment_analysis 9.81 0.08 9.93
EnrichedGeneView 9.06 0.08 9.52
ScatterView 9.08 0.00 9.07
ReadRRA 8.69 0.00 8.69
SquareView 8.41 0.01 8.42
enrich.HGT 8.28 0.05 8.33
CellCycleView 7.86 0.45 8.41
TransGeneID 8.02 0.06 21.82
ReadBeta 7.64 0.02 7.66
ViolinView 7.31 0.02 7.33
DensityView 7.20 0.02 7.22
EnrichSquare 7.11 0.05 7.15
VolcanoView 7.15 0.00 7.15
DensityDiffView 7.08 0.00 7.08
HeatmapView 6.88 0.03 6.91
NormalizeBeta 6.59 0.00 6.59
EnrichAB 6.55 0.00 6.55
normalize.loess 6.25 0.00 6.25
getOrg 5.92 0.01 5.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
enrich.ORT 17.89 0.06 17.96
arrangePathview 16.70 0.66 18.48
RankView 12.78 0.05 12.83
MAView 12.08 0.64 12.71
enrichment_analysis 10.65 0.13 10.76
EnrichedView 9.89 0.05 9.93
VolcanoView 9.74 0.03 9.77
ReadRRA 9.39 0.05 9.44
enrich.HGT 9.40 0.03 9.45
CellCycleView 9.04 0.19 9.23
DensityDiffView 8.75 0.03 8.78
EnrichedGeneView 8.41 0.04 8.42
ScatterView 8.29 0.05 8.33
ReadBeta 8.17 0.09 8.26
SquareView 7.72 0.00 7.72
getOrg 7.45 0.03 7.49
DensityView 7.09 0.08 7.18
normalize.loess 7.11 0.04 7.15
HeatmapView 7.03 0.01 7.05
ViolinView 6.89 0.06 6.95
EnrichSquare 6.42 0.07 6.49
EnrichAB 6.33 0.04 6.37
TransGeneID 6.26 0.02 19.81
NormalizeBeta 6.22 0.05 6.27
* 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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/MAGeCKFlute.Rcheck/00check.log'
for details.
MAGeCKFlute.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MAGeCKFlute_1.2.3.tar.gz && rm -rf MAGeCKFlute.buildbin-libdir && mkdir MAGeCKFlute.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAGeCKFlute.buildbin-libdir MAGeCKFlute_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MAGeCKFlute_1.2.3.zip && rm MAGeCKFlute_1.2.3.tar.gz MAGeCKFlute_1.2.3.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 9347k 100 9347k 0 0 67.2M 0 --:--:-- --:--:-- --:--:-- 69.1M
install for i386
* installing *source* package 'MAGeCKFlute' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MAGeCKFlute'
finding HTML links ... done
BatchRemove html
CellCycleView html
CorrView html
CutoffCalling html
DensityDiffView html
DensityView html
EnrichAB html
EnrichSquare html
EnrichedGSEView html
EnrichedGeneView html
EnrichedView html
FluteMLE html
FluteRRA html
HeatmapView html
IdentBarView html
KeggPathwayView html
finding level-2 HTML links ... done
MAView html
MapRatesView html
NormalizeBeta html
RankView html
ReadBeta html
ReadRRA html
ReadsgRRA html
ScatterView html
Selector html
SquareView html
TransGeneID html
ViolinView html
VolcanoView html
Zuber_Essential html
arrangePathview html
countsummary html
enrich.GSE html
enrich.HGT html
enrich.ORT html
enrichment_analysis html
getOrg html
mle.gene_summary html
noEnrichPlot html
normalize.loess html
readGMT html
rra.gene_summary html
rra.sgrna_summary html
sgRankView html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'MAGeCKFlute' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MAGeCKFlute' as MAGeCKFlute_1.2.3.zip
* DONE (MAGeCKFlute)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MAGeCKFlute' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
MAGeCKFlute.Rcheck/examples_i386/MAGeCKFlute-Ex.timings
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MAGeCKFlute.Rcheck/examples_x64/MAGeCKFlute-Ex.timings
|