Wubing Zhang
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 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 2019-04-16 12:04:05 -0400 (Tue, 16 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 | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MAGeCKFlute |
| Version: 1.2.3 |
| 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_1.2.3.tar.gz |
| StartedAt: 2019-04-16 00:58:16 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:07:40 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 564.3 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_1.2.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MAGeCKFlute.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.3’
* 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 ... NOTE
Found the following non-portable file paths:
MAGeCKFlute/vignettes/MAGeCKFlute_cache/html/CheckCountSummary_772d2f34111dd8efb7ea46fc8b46e5b8.RData
MAGeCKFlute/vignettes/MAGeCKFlute_cache/html/EstimateCellCycle_2d76364f66438e955d3cbfef21e61b9d.RData
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MAGeCKFlute’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.3Mb
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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
arrangePathview 23.123 0.685 25.714
enrich.ORT 20.375 0.236 20.773
MAView 19.414 0.224 19.807
EnrichedGeneView 18.617 0.259 17.226
EnrichedView 13.776 0.363 14.216
DensityView 12.980 0.182 13.469
EnrichSquare 12.473 0.259 13.024
RankView 12.327 0.135 12.573
SquareView 12.251 0.189 12.563
EnrichAB 12.273 0.130 12.631
enrichment_analysis 12.029 0.190 12.332
enrich.HGT 11.798 0.246 12.154
ViolinView 11.658 0.211 12.025
VolcanoView 11.635 0.152 11.858
ReadRRA 11.476 0.120 11.756
normalize.loess 11.334 0.137 11.484
CellCycleView 11.227 0.233 11.538
ScatterView 11.271 0.171 11.561
DensityDiffView 11.284 0.142 11.526
ReadBeta 11.141 0.111 11.458
NormalizeBeta 10.502 0.146 10.722
getOrg 10.189 0.094 10.309
TransGeneID 10.131 0.146 25.907
HeatmapView 9.929 0.122 10.164
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.8-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/3.5/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 | 0.905 | 0.034 | 0.948 | |
| CellCycleView | 11.227 | 0.233 | 11.538 | |
| CorrView | 0.736 | 0.010 | 0.754 | |
| CutoffCalling | 0.003 | 0.000 | 0.004 | |
| DensityDiffView | 11.284 | 0.142 | 11.526 | |
| DensityView | 12.980 | 0.182 | 13.469 | |
| EnrichAB | 12.273 | 0.130 | 12.631 | |
| EnrichSquare | 12.473 | 0.259 | 13.024 | |
| EnrichedGSEView | 0.000 | 0.001 | 0.000 | |
| EnrichedGeneView | 18.617 | 0.259 | 17.226 | |
| EnrichedView | 13.776 | 0.363 | 14.216 | |
| FluteMLE | 0.001 | 0.002 | 0.004 | |
| FluteRRA | 0.002 | 0.001 | 0.003 | |
| HeatmapView | 9.929 | 0.122 | 10.164 | |
| IdentBarView | 0.214 | 0.003 | 0.217 | |
| KeggPathwayView | 0.021 | 0.005 | 0.027 | |
| MAView | 19.414 | 0.224 | 19.807 | |
| MapRatesView | 0.546 | 0.005 | 0.560 | |
| NormalizeBeta | 10.502 | 0.146 | 10.722 | |
| RankView | 12.327 | 0.135 | 12.573 | |
| ReadBeta | 11.141 | 0.111 | 11.458 | |
| ReadRRA | 11.476 | 0.120 | 11.756 | |
| ReadsgRRA | 0.868 | 0.049 | 0.925 | |
| ScatterView | 11.271 | 0.171 | 11.561 | |
| Selector | 0.277 | 0.005 | 0.287 | |
| SquareView | 12.251 | 0.189 | 12.563 | |
| TransGeneID | 10.131 | 0.146 | 25.907 | |
| ViolinView | 11.658 | 0.211 | 12.025 | |
| VolcanoView | 11.635 | 0.152 | 11.858 | |
| arrangePathview | 23.123 | 0.685 | 25.714 | |
| countsummary | 0.007 | 0.002 | 0.009 | |
| enrich.GSE | 0.013 | 0.000 | 0.013 | |
| enrich.HGT | 11.798 | 0.246 | 12.154 | |
| enrich.ORT | 20.375 | 0.236 | 20.773 | |
| enrichment_analysis | 12.029 | 0.190 | 12.332 | |
| getOrg | 10.189 | 0.094 | 10.309 | |
| mle.gene_summary | 0.034 | 0.006 | 0.040 | |
| normalize.loess | 11.334 | 0.137 | 11.484 | |
| rra.gene_summary | 0.028 | 0.005 | 0.033 | |
| rra.sgrna_summary | 0.155 | 0.021 | 0.176 | |
| sgRankView | 0.564 | 0.037 | 0.602 | |