Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O [P] Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for PAA on oaxaca

This page was generated on 2015-10-27 17:41:49 -0400 (Tue, 27 Oct 2015).

Package 740/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAA 1.4.0
Michael Turewicz , Martin Eisenacher
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/PAA
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: PAA
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PAA_1.4.0.tar.gz
StartedAt: 2015-10-27 06:20:44 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 06:24:10 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 205.8 seconds
RetCode: 0
Status:  OK 
CheckDir: PAA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PAA_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PAA.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 ‘PAA/DESCRIPTION’ ... OK
* this is package ‘PAA’ 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 ‘PAA’ can be installed ... [30s/31s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/9s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/PAA.Rcheck/00check.log’
for details.


PAA.Rcheck/00install.out:

* installing *source* package ‘PAA’ ...
** 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 PAA_init.c -o PAA_init.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++ -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 joinMCountResults.cpp -o joinMCountResults.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 mCount.cpp -o mCount.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 mMsMatrix.cpp -o mMsMatrix.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 sampling.cpp -o sampling.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 PAA.so PAA_init.o RcppExports.o joinMCountResults.o mCount.o mMsMatrix.o sampling.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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
batchAdjust0.7280.0300.759
batchFilter1.3250.0411.367
diffAnalysis1.8900.0822.006
loadGPR0.2220.0060.229
mMsMatrix0.0000.0000.001
normalizeArrays0.2340.0110.246
plotFeatures0.3850.0140.400
plotFeaturesHeatmap0.2550.0140.269
plotMAPlots0.8810.0240.907
plotNormMethods0.5500.0150.567
preselect1.4080.0551.466
printFeatures0.4100.0170.427
pvaluePlot1.2420.0141.257
selectFeatures1.6880.0191.707
shuffleData0.2240.0110.234
volcanoPlot1.6430.0201.664