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BioC 3.2: CHECK report for IMPCdata on oaxaca

This page was generated on 2016-04-23 10:28:29 -0700 (Sat, 23 Apr 2016).

Package 526/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IMPCdata 1.4.0
Jeremy Mason
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/IMPCdata
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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: IMPCdata
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.4.0.tar.gz
StartedAt: 2016-04-23 01:19:53 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:23:27 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 213.2 seconds
RetCode: 0
Status:  OK 
CheckDir: IMPCdata.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/IMPCdata.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IMPCdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IMPCdata’ version ‘1.4.0’
* 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 ‘IMPCdata’ can be installed ... [1s/1s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/200s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
printAlleles     0.143  0.034  31.496
printGenes       0.135  0.033  31.000
getAlleles       0.133  0.034  37.378
getGenes         0.123  0.032  34.605
getParameters    0.038  0.009   8.591
printParameters  0.036  0.009   8.855
printProcedures  0.035  0.009   8.652
getProcedures    0.033  0.008   8.748
printPhenCenters 0.020  0.007   9.488
getPhenCenters   0.010  0.004   5.232
* 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

IMPCdata.Rcheck/00install.out:

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

IMPCdata.Rcheck/IMPCdata-Ex.timings:

nameusersystemelapsed
getAlleles 0.133 0.03437.378
getGenes 0.123 0.03234.605
getIMPCDataset0.4220.0134.013
getIMPCTable0.0080.0022.148
getName0.0010.0010.746
getParameters0.0380.0098.591
getPhenCenters0.0100.0045.232
getPipelines0.0040.0021.779
getProcedures0.0330.0088.748
getStrains0.0070.0022.111
getZygosities0.0020.0010.309
printAlleles 0.143 0.03431.496
printGenes 0.135 0.03331.000
printParameters0.0360.0098.855
printPhenCenters0.0200.0079.488
printPipelines0.0040.0011.411
printProcedures0.0350.0098.652
printStrains0.0060.0012.397