BioC 3.5: CHECK report for pcaExplorer on malbec2
This page was generated on 2017-10-18 14:17:40 -0400 (Wed, 18 Oct 2017).
pcaExplorer 2.2.1 Federico Marini
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | URL: https://git.bioconductor.org/packages/pcaExplorer | Branch: RELEASE_3_5 | Last Commit: a36b15e | Last Changed Date: 2017-08-28 15:22:23 -0400 (Mon, 28 Aug 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Package: pcaExplorer |
Version: 2.2.1 |
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pcaExplorer_2.2.1.tar.gz |
StartedAt: 2017-10-18 01:23:18 -0400 (Wed, 18 Oct 2017) |
EndedAt: 2017-10-18 01:28:15 -0400 (Wed, 18 Oct 2017) |
EllapsedTime: 296.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pcaExplorer.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pcaExplorer_2.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/pcaExplorer.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pcaExplorer’ version ‘2.2.1’
* 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 ‘pcaExplorer’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
doc 4.8Mb
* 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
pcaExplorer: no visible binding for '<<-' assignment to
‘pcaexplorer_env’
pcaExplorer : <anonymous>: no visible binding for global variable
‘airway’
pcaExplorer : <anonymous>: no visible binding for global variable
‘pcaexplorer_env’
Undefined global functions or variables:
airway pcaexplorer_env
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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-3.5-bioc/meat/pcaExplorer.Rcheck/00check.log’
for details.
pcaExplorer.Rcheck/00install.out:
* installing *source* package ‘pcaExplorer’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pcaExplorer)
pcaExplorer.Rcheck/pcaExplorer-Ex.timings:
name | user | system | elapsed
|
correlatePCs | 3.592 | 0.032 | 3.627 |
|
distro_expr | 3.860 | 0.008 | 3.871 |
|
geneprofiler | 1.844 | 0.000 | 1.847 |
|
genespca | 3.388 | 0.000 | 3.390 |
|
get_annotation | 3.864 | 0.032 | 3.942 |
|
get_annotation_orgdb | 2.248 | 0.012 | 2.263 |
|
hi_loadings | 1.776 | 0.000 | 1.775 |
|
limmaquickpca2go | 1.692 | 0.028 | 1.721 |
|
makeExampleDESeqDataSet_multifac | 0.104 | 0.000 | 0.106 |
|
pair_corr | 1.736 | 0.008 | 1.746 |
|
pca2go | 1.812 | 0.004 | 1.818 |
|
pcaExplorer | 2.084 | 0.012 | 2.098 |
|
pcaplot | 2.496 | 0.000 | 2.497 |
|
pcaplot3d | 1.944 | 0.008 | 2.044 |
|
pcascree | 2.088 | 0.000 | 2.093 |
|
plotPCcorrs | 2.180 | 0.000 | 2.183 |
|
topGOtable | 1.972 | 0.012 | 1.985 |
|