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BioC 3.0: CHECK report for PAA on zin1

This page was generated on 2015-04-10 09:42:42 -0700 (Fri, 10 Apr 2015).

Package 633/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAA 1.0.0
Michael Turewicz , Martin Eisenacher
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PAA
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: PAA
Version: 1.0.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings PAA_1.0.0.tar.gz
StartedAt: 2015-04-10 02:45:47 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:50:08 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 261.5 seconds
RetCode: 0
Status:  OK 
CheckDir: PAA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings PAA_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/PAA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAA/DESCRIPTION’ ... OK
* this is package ‘PAA’ version ‘1.0.0’
* 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 ‘PAA’ can be installed ... [37s/38s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Michael Turewicz <michael.turewicz@rub.de> [aut, cre]
  Martin Eisenacher <martin.eisenacher@rub.de> [ctb, cre]
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/49s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
printFeatures       6.248  0.000   6.340
plotFeaturesHeatmap 6.064  0.000   6.077
plotFeatures        6.013  0.012   6.041
selectFeatures      5.992  0.000   6.026
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/10s]
 [10s/11s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/PAA.Rcheck/00check.log’
for details.

PAA.Rcheck/00install.out:

* installing *source* package ‘PAA’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c PAA_init.c -o PAA_init.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c joinMCountResults.cpp -o joinMCountResults.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mCount.cpp -o mCount.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mMsMatrix.cpp -o mMsMatrix.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c sampling.cpp -o sampling.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o PAA.so PAA_init.o RcppExports.o joinMCountResults.o mCount.o mMsMatrix.o sampling.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/PAA.Rcheck/PAA/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PAA)

PAA.Rcheck/PAA-Ex.timings:

nameusersystemelapsed
batchAdjust0.5120.0040.541
batchFilter1.5680.0041.712
diffAnalysis1.5240.0161.572
loadGPR0.0920.0000.091
mMsMatrix0.0000.0000.001
normalizeArrays0.0920.0040.097
plotFeatures6.0130.0126.041
plotFeaturesHeatmap6.0640.0006.077
plotMAPlots4.6840.0284.886
plotNormMethods3.7530.0203.781
preselect1.0680.0281.120
printFeatures6.2480.0006.340
pvaluePlot1.1800.0001.188
selectFeatures5.9920.0006.026
shuffleData0.0600.0040.063
volcanoPlot1.4050.0041.408