Wubing Zhang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/MAGeCKFlute |
| Branch: RELEASE_3_7 |
| Last Commit: 87b8287 |
| Last Changed Date: 2018-10-05 03:13:41 -0400 (Fri, 05 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:59:18 -0400 (Wed, 17 Oct 2018).
| Package 819/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAGeCKFlute 1.0.1 Wubing Zhang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MAGeCKFlute |
| Version: 1.0.1 |
| 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_1.0.1.tar.gz |
| StartedAt: 2018-10-16 22:19:51 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 22:28:43 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 532.2 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_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MAGeCKFlute.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.1’
* 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 6.9Mb
sub-directories of 1Mb or more:
doc 1.4Mb
extdata 4.7Mb
* 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 ‘Name’
EnrichedGSEView: no visible binding for global variable ‘logP’
EnrichedView: no visible binding for global variable ‘logP’
EnrichedView: no visible binding for global variable ‘Name’
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’
TransGeneID: no visible binding for global variable ‘bods’
ViolinView: no visible binding for global variable ‘variable’
ViolinView: no visible binding for global variable ‘value’
enrich.DAVID: no visible global function definition for ‘qvalue’
getOrg: no visible binding for global variable ‘bods’
Undefined global functions or variables:
..density.. Control Count Diff Gene GeneNum NES Name PC1 PC2 Rank
Treatment Zuber_Essential bods category count group keggConv logP
parseKGML2Graph2 percent pos qvalue r rn.list shape value variable x
y
* 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 22.665 0.308 56.028
EnrichedView 13.323 0.361 41.759
enrichment_analysis 12.198 0.261 26.604
enrich.HGT 11.779 0.228 39.248
TransGeneID 11.493 0.139 36.123
getOrg 11.421 0.115 11.663
MAView 9.333 0.110 9.495
NormalizeBeta 1.633 0.071 37.169
ReadRRA 0.477 0.030 32.544
* 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
‘/Users/biocbuild/bbs-3.7-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 | 2.897 | 0.060 | 2.978 | |
| CellCycleView | 1.185 | 0.052 | 1.249 | |
| CorrView | 0.626 | 0.009 | 0.637 | |
| DensityDiffView | 0.433 | 0.019 | 0.456 | |
| DensityView | 0.878 | 0.052 | 0.940 | |
| EnrichedGSEView | 0.001 | 0.000 | 0.001 | |
| EnrichedView | 13.323 | 0.361 | 41.759 | |
| FluteMLE | 0.003 | 0.001 | 0.006 | |
| FluteRRA | 0.012 | 0.003 | 0.015 | |
| HeatmapView | 0.177 | 0.005 | 0.185 | |
| IdentBarView | 0.233 | 0.001 | 0.238 | |
| KeggPathwayView | 0.021 | 0.004 | 0.026 | |
| MAView | 9.333 | 0.110 | 9.495 | |
| MLE_Data | 0.017 | 0.003 | 0.020 | |
| MapRatesView | 0.529 | 0.004 | 0.542 | |
| NormalizeBeta | 1.633 | 0.071 | 37.169 | |
| RRA_Data | 0.009 | 0.002 | 0.011 | |
| RankView | 1.687 | 0.049 | 1.763 | |
| ReadBeta | 0.035 | 0.006 | 0.041 | |
| ReadRRA | 0.477 | 0.030 | 32.544 | |
| ScatterView | 0.702 | 0.057 | 0.770 | |
| Selector | 0.366 | 0.005 | 0.379 | |
| SquareView | 1.829 | 0.104 | 1.947 | |
| TransGeneID | 11.493 | 0.139 | 36.123 | |
| ViolinView | 1.994 | 0.197 | 2.215 | |
| arrangePathview | 0.002 | 0.001 | 0.002 | |
| enrich.DAVID | 0.01 | 0.00 | 0.01 | |
| enrich.GOstats | 0.010 | 0.001 | 0.010 | |
| enrich.GSE | 0.01 | 0.00 | 0.01 | |
| enrich.HGT | 11.779 | 0.228 | 39.248 | |
| enrich.ORT | 22.665 | 0.308 | 56.028 | |
| enrichment_analysis | 12.198 | 0.261 | 26.604 | |
| getOrg | 11.421 | 0.115 | 11.663 | |
| normalize.loess | 1.305 | 0.021 | 1.338 | |