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 11:53:12 -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: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MAGeCKFlute_1.2.3.tar.gz |
| StartedAt: 2019-04-16 01:05:37 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:13:49 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 491.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAGeCKFlute.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MAGeCKFlute_1.2.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MAGeCKFlute.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.3’
* 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 ... OK
* 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 22.992 0.340 25.243
enrich.ORT 18.768 0.008 18.866
MAView 15.748 0.048 15.848
EnrichedView 15.584 0.020 15.770
EnrichedGeneView 15.052 0.012 14.922
RankView 12.580 0.004 12.631
enrich.HGT 12.220 0.008 12.246
enrichment_analysis 11.424 0.020 11.463
CellCycleView 11.304 0.112 11.455
ReadRRA 11.164 0.004 11.217
ScatterView 10.924 0.016 11.003
SquareView 10.920 0.020 10.981
NormalizeBeta 10.716 0.004 10.764
TransGeneID 10.468 0.000 29.397
DensityDiffView 10.232 0.012 10.258
EnrichSquare 10.224 0.008 10.319
VolcanoView 10.076 0.028 10.138
ReadBeta 10.100 0.000 10.145
EnrichAB 9.820 0.004 9.851
ViolinView 9.688 0.020 9.736
HeatmapView 9.628 0.000 9.685
DensityView 9.480 0.020 9.526
getOrg 8.224 0.000 8.236
normalize.loess 8.136 0.008 8.155
* 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-3.8-bioc/meat/MAGeCKFlute.Rcheck/00check.log’
for details.
MAGeCKFlute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MAGeCKFlute ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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 | 1.124 | 0.092 | 1.262 | |
| CellCycleView | 11.304 | 0.112 | 11.455 | |
| CorrView | 0.632 | 0.020 | 0.657 | |
| CutoffCalling | 0.008 | 0.000 | 0.005 | |
| DensityDiffView | 10.232 | 0.012 | 10.258 | |
| DensityView | 9.480 | 0.020 | 9.526 | |
| EnrichAB | 9.820 | 0.004 | 9.851 | |
| EnrichSquare | 10.224 | 0.008 | 10.319 | |
| EnrichedGSEView | 0.000 | 0.000 | 0.001 | |
| EnrichedGeneView | 15.052 | 0.012 | 14.922 | |
| EnrichedView | 15.584 | 0.020 | 15.770 | |
| FluteMLE | 0.000 | 0.000 | 0.001 | |
| FluteRRA | 0.000 | 0.000 | 0.002 | |
| HeatmapView | 9.628 | 0.000 | 9.685 | |
| IdentBarView | 0.212 | 0.000 | 0.213 | |
| KeggPathwayView | 0.024 | 0.000 | 0.054 | |
| MAView | 15.748 | 0.048 | 15.848 | |
| MapRatesView | 0.512 | 0.000 | 0.512 | |
| NormalizeBeta | 10.716 | 0.004 | 10.764 | |
| RankView | 12.580 | 0.004 | 12.631 | |
| ReadBeta | 10.100 | 0.000 | 10.145 | |
| ReadRRA | 11.164 | 0.004 | 11.217 | |
| ReadsgRRA | 0.396 | 0.008 | 0.404 | |
| ScatterView | 10.924 | 0.016 | 11.003 | |
| Selector | 0.352 | 0.000 | 0.353 | |
| SquareView | 10.920 | 0.020 | 10.981 | |
| TransGeneID | 10.468 | 0.000 | 29.397 | |
| ViolinView | 9.688 | 0.020 | 9.736 | |
| VolcanoView | 10.076 | 0.028 | 10.138 | |
| arrangePathview | 22.992 | 0.340 | 25.243 | |
| countsummary | 0.008 | 0.000 | 0.006 | |
| enrich.GSE | 0.016 | 0.000 | 0.013 | |
| enrich.HGT | 12.220 | 0.008 | 12.246 | |
| enrich.ORT | 18.768 | 0.008 | 18.866 | |
| enrichment_analysis | 11.424 | 0.020 | 11.463 | |
| getOrg | 8.224 | 0.000 | 8.236 | |
| mle.gene_summary | 0.116 | 0.004 | 0.122 | |
| normalize.loess | 8.136 | 0.008 | 8.155 | |
| rra.gene_summary | 0.02 | 0.00 | 0.02 | |
| rra.sgrna_summary | 0.128 | 0.000 | 0.129 | |
| sgRankView | 0.408 | 0.004 | 0.410 | |