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BioC 3.1: CHECK report for NanoStringQCPro on zin2

This page was generated on 2015-10-09 09:26:55 -0700 (Fri, 09 Oct 2015).

Package 646/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringQCPro 1.0.2
Robert Ziman
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/NanoStringQCPro
Last Changed Rev: 107407 / Revision: 109384
Last Changed Date: 2015-08-13 16:53:03 -0700 (Thu, 13 Aug 2015)
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
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NanoStringQCPro
Version: 1.0.2
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings NanoStringQCPro_1.0.2.tar.gz
StartedAt: 2015-10-09 03:53:38 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:55:28 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 110.0 seconds
RetCode: 0
Status:  OK 
CheckDir: NanoStringQCPro.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings NanoStringQCPro_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/NanoStringQCPro.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoStringQCPro/DESCRIPTION’ ... OK
* this is package ‘NanoStringQCPro’ version ‘1.0.2’
* 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 ‘NanoStringQCPro’ can be installed ... [9s/9s] 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 ... [18s/18s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
makeQCReport 12.192  0.114  12.371
* 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

NanoStringQCPro.Rcheck/00install.out:

* installing *source* package ‘NanoStringQCPro’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (NanoStringQCPro)

NanoStringQCPro.Rcheck/NanoStringQCPro-Ex.timings:

nameusersystemelapsed
RccSet-class0.4920.0000.491
addCodesetAnnotation0.2680.0040.272
buildCodesetAnnotation0.0090.0000.009
checkRccSet0.0030.0000.003
contentNorm0.0910.0000.091
copyRccSet0.0190.0000.019
getBackground0.010.000.01
getBlankLabel0.0020.0000.002
makeQCReport12.192 0.11412.371
newRccSet0.2490.0080.258
posCtrlNorm0.0240.0000.024
preprocRccSet0.0810.0000.081
presAbsCall0.0590.0000.060
readCdrDesignData0.0030.0000.002
readRcc0.0040.0000.004
readRlf0.0040.0000.004
subtractBackground0.0920.0000.092