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BioC 3.2: CHECK report for Rqc on oaxaca

This page was generated on 2015-10-27 17:41:55 -0400 (Tue, 27 Oct 2015).

Package 912/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rqc 1.4.0
Welliton Souza
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rqc
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: Rqc
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rqc_1.4.0.tar.gz
StartedAt: 2015-10-27 07:32:53 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 07:38:02 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 308.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Rqc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rqc_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rqc.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rqc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rqc’ 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 ‘Rqc’ can be installed ... [26s/27s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [78s/72s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Rqc-package 18.658  1.427  17.602
rqc         17.281  1.533  16.336
rqcReport   15.013  0.351  14.685
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [12s/12s]
 [12s/12s] 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

Rqc.Rcheck/00install.out:

* installing *source* package ‘Rqc’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RRDNA.cpp -o RRDNA.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/Rqc.Rcheck/Rqc/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rqc)

Rqc.Rcheck/Rqc-Ex.timings:

nameusersystemelapsed
Rqc-package18.658 1.42717.602
RqcResultSet-class0.4160.0030.420
checkpoint0.0030.0010.003
detectFileFormat0.0050.0000.005
fromRRDNA0.0020.0000.001
matdist0.0010.0000.001
rqc17.281 1.53316.336
rqcCycleAverageQualityPcaPlot0.8450.0600.905
rqcCycleAverageQualityPlot0.3670.0050.372
rqcCycleBaseCallsPlot0.6080.0050.615
rqcCycleGCPlot0.3000.0020.318
rqcCycleQualityBoxPlot3.5800.0073.590
rqcCycleQualityPlot2.1220.0252.149
rqcFileHeatmap0.0570.0020.061
rqcGroupCycleAverageQualityPlot0.3090.0010.311
rqcQA0.1960.0010.197
rqcReadFrequencyPlot0.2400.0020.241
rqcReadQualityBoxPlot0.3740.0010.376
rqcReadQualityPlot0.3020.0010.304
rqcReadWidthPlot0.2490.0020.250
rqcReport15.013 0.35114.685
rqcShinyReport0.0030.0000.003
stats4trim0.4250.0060.432
subsetByGroup1.0330.0231.056
toRRDNA0.0010.0000.001