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BioC 3.4: CHECK report for BatchQC on morelia

This page was generated on 2017-04-15 16:27:40 -0400 (Sat, 15 Apr 2017).

Package 86/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 1.2.1
Solaiappan Manimaran
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BatchQC
Last Changed Rev: 124428 / Revision: 128728
Last Changed Date: 2016-11-23 23:11:06 -0500 (Wed, 23 Nov 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BatchQC
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_1.2.1.tar.gz
StartedAt: 2017-04-14 22:56:00 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:58:53 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 172.8 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_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BatchQC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.1’
* 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 ‘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 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
Examples with CPU or elapsed time > 5s
         user system elapsed
batchQC 5.135  0.285   5.687
* 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
batchQC5.1350.2855.687
batchQC_analyze0.2960.0140.311
batchQC_condition_adjusted0.0520.0110.063
batchQC_filter_genes0.0690.0020.071
batchQC_fsva_adjusted0.2270.0120.264
batchQC_num.sv0.1470.0010.148
batchQC_shapeVariation0.1130.0010.115
batchQC_sva0.2120.0020.215
batchQC_svregress_adjusted0.2050.0150.222
batchqc_circosplot0.1750.0010.176
batchqc_correlation0.2500.0030.253
batchqc_corscatter0.0660.0010.067
batchqc_explained_variation0.0470.0040.051
batchqc_heatmap0.2610.0020.264
batchqc_pc_explained_variation0.0580.0040.064
batchqc_pca0.0530.0090.062
batchqc_pca_svd0.2810.0030.287
batchtest0.0940.0060.099
combatPlot0.0600.0020.064
getShinyInput0.0750.0440.120
getShinyInputCombat0.0000.0000.001
getShinyInputOrig0.0620.0370.099
getShinyInputSVA0.0010.0000.001
getShinyInputSVAf0.0000.0000.001
getShinyInputSVAr0.0000.0000.001
gnormalize0.0010.0000.001
log2CPM0.0810.0110.093
rnaseq_sim0.2780.0580.335
setShinyInput000
setShinyInputCombat0.0000.0000.001
setShinyInputOrig0.0010.0010.001
setShinyInputSVA0.0010.0000.001
setShinyInputSVAf0.0010.0000.000
setShinyInputSVAr0.0010.0000.001