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BioC 3.3: CHECK report for BatchQC on oaxaca

This page was generated on 2016-10-13 13:03:10 -0700 (Thu, 13 Oct 2016).

Package 79/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 1.0.22
Solaiappan Manimaran
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/BatchQC
Last Changed Rev: 120633 / Revision: 122332
Last Changed Date: 2016-08-31 17:15:14 -0700 (Wed, 31 Aug 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BatchQC
Version: 1.0.22
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_1.0.22.tar.gz
StartedAt: 2016-10-12 23:28:20 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:31:04 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 163.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BatchQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_1.0.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/BatchQC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BatchQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BatchQC’ version ‘1.0.22’
* 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 ‘BatchQC’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... 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: OK

BatchQC.Rcheck/00install.out:

* installing *source* package ‘BatchQC’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BatchQC)

BatchQC.Rcheck/BatchQC-Ex.timings:

nameusersystemelapsed
batchQC4.2220.2854.664
batchQC_analyze0.2460.0110.258
batchQC_condition_adjusted0.0410.0090.050
batchQC_filter_genes0.0520.0010.053
batchQC_fsva_adjusted0.2060.0120.219
batchQC_num.sv0.1220.0040.126
batchQC_shapeVariation0.0980.0030.100
batchQC_sva0.1940.0030.198
batchQC_svregress_adjusted0.2030.0090.213
batchqc_circosplot0.1630.0010.164
batchqc_correlation0.2490.0020.250
batchqc_corscatter0.0730.0010.076
batchqc_explained_variation0.0450.0020.047
batchqc_heatmap0.2190.0030.222
batchqc_pc_explained_variation0.0570.0030.061
batchqc_pca0.0540.0080.063
batchqc_pca_svd0.2280.0030.232
batchtest0.0870.0070.094
combatPlot0.0590.0020.062
getShinyInput0.0700.0410.111
getShinyInputCombat0.0010.0000.001
getShinyInputOrig0.0640.0350.099
getShinyInputSVA0.0010.0000.001
getShinyInputSVAf0.0010.0010.001
getShinyInputSVAr0.0010.0000.001
gnormalize0.0020.0000.002
log2CPM0.0700.0090.079
rnaseq_sim0.2310.0510.281
setShinyInput000
setShinyInputCombat0.0010.0000.000
setShinyInputOrig0.0000.0010.000
setShinyInputSVA000
setShinyInputSVAf0.0010.0000.000
setShinyInputSVAr0.0010.0000.000