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 12:40:11 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGeCKFlute.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.4.3.tar.gz |
| StartedAt: 2019-10-16 04:53:23 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:03:11 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 587.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAGeCKFlute.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGeCKFlute.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.4.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MAGeCKFlute.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.4.3'
* 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 whether package 'MAGeCKFlute' can be installed ... OK
* checking installed package size ... NOTE
installed size is 16.5Mb
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
* 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
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EnrichAnalyzer 17.09 0.81 20.56
enrich.ORT 16.92 0.11 17.03
EnrichedFilter 13.38 0.28 13.66
EnrichedGeneView 12.97 0.08 13.05
arrangePathview 11.41 0.59 12.81
enrich.HGT 10.86 0.05 10.91
MAView 6.57 0.65 7.25
getOrg 6.41 0.05 6.45
gsGetter 6.19 0.14 6.32
TransGeneID 5.71 0.00 5.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EnrichAnalyzer 22.16 0.34 22.52
enrich.ORT 18.65 0.11 18.77
enrich.HGT 16.44 0.11 16.55
EnrichedGeneView 15.74 0.02 15.75
arrangePathview 13.63 0.42 15.19
EnrichedFilter 12.98 0.06 13.05
TransGeneID 11.67 0.00 11.67
getOrg 9.16 0.01 9.23
gsGetter 7.97 0.16 8.14
MAView 6.14 0.74 6.87
* 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-3.9-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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MAGeCKFlute_1.4.3.tar.gz && rm -rf MAGeCKFlute.buildbin-libdir && mkdir MAGeCKFlute.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAGeCKFlute.buildbin-libdir MAGeCKFlute_1.4.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MAGeCKFlute_1.4.3.zip && rm MAGeCKFlute_1.4.3.tar.gz MAGeCKFlute_1.4.3.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 14.7M 100 14.7M 0 0 74.7M 0 --:--:-- --:--:-- --:--:-- 77.7M
install for i386
* 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
converting help for package 'MAGeCKFlute'
finding HTML links ... done
BatchRemove html
CellCycleView html
CutoffCalling html
DensityDiffView html
DensityView html
EnrichAB html
EnrichAnalyzer html
EnrichSquare html
EnrichedFilter 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
getOrg html
gsGetter 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'MAGeCKFlute' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MAGeCKFlute' as MAGeCKFlute_1.4.3.zip
* DONE (MAGeCKFlute)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MAGeCKFlute' successfully unpacked and MD5 sums checked
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MAGeCKFlute.Rcheck/examples_i386/MAGeCKFlute-Ex.timings
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MAGeCKFlute.Rcheck/examples_x64/MAGeCKFlute-Ex.timings
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