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BioC 3.1: CHECK report for MIMOSA on morelia

This page was generated on 2015-10-09 09:41:35 -0700 (Fri, 09 Oct 2015).

Package 600/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIMOSA 1.6.0
Greg Finak
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/MIMOSA
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 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: MIMOSA
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MIMOSA_1.6.0.tar.gz
StartedAt: 2015-10-09 03:56:10 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:57:49 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 99.5 seconds
RetCode: 0
Status:  OK 
CheckDir: MIMOSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MIMOSA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/MIMOSA.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 ‘MIMOSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MIMOSA’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MIMOSA’ can be installed ... [23s/24s] 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 ... NOTE
MIMOSAExpressionSet: no visible global function definition for
  ‘ExpressionSet’
MIMOSAExpressionSet: no visible global function definition for
  ‘AnnotatedDataFrame’
boxplotMIMOSAResultList: no visible global function definition for
  ‘ldply’
boxplotMIMOSAResultList: no visible global function definition for
  ‘aes’
boxplotMIMOSAResultList: no visible binding for global variable
  ‘Proportion’
boxplotMIMOSAResultList: no visible binding for global variable
  ‘Proportion_REF’
boxplotMIMOSAResultList: no visible global function definition for
  ‘geom_boxplot’
boxplotMIMOSAResultList: no visible global function definition for
  ‘coord_trans’
boxplotMIMOSAResultList: no visible global function definition for
  ‘facet_wrap’
boxplotMIMOSAResultList: no visible global function definition for
  ‘ggtitle’
boxplotMIMOSAResultList: no visible global function definition for
  ‘geom_jitter’
boxplotMIMOSAResultList: no visible global function definition for
  ‘position_jitter’
boxplotMIMOSAResultList: no visible global function definition for
  ‘scale_fill_brewer’
boxplotMIMOSAResultList: no visible global function definition for
  ‘scale_color_brewer’
boxplotMIMOSAResultList: no visible global function definition for
  ‘geom_line’
boxplotMIMOSAResultList: no visible binding for global variable ‘PTID’
huberFilter: no visible global function definition for ‘huber’
refactorPData: no visible global function definition for ‘pData<-’
setpData.icsdata: no visible global function definition for ‘pData<-’
volcanoPlot.MIMOSAResultList: no visible global function definition for
  ‘is.formula’
volcanoPlot.MIMOSAResultList: no visible global function definition for
  ‘facet_grid’
MIMOSA,formula-ExpressionSet : .local: no visible binding for global
  variable ‘RefTreat’
MIMOSA,formula-ExpressionSet : .local: no visible global function
  definition for ‘mclapply’
pData<-,BetaMixResult-data.frame: no visible global function definition
  for ‘pData<-’
* 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 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 ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
MIMOSA-accessors 5.581  0.133   5.715
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [5s/5s]
 [5s/5s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/MIMOSA.Rcheck/00check.log’
for details.


MIMOSA.Rcheck/00install.out:

* installing *source* package ‘MIMOSA’ ...
** 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" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "RcppArmadillo:::CxxFlags()"`   -fPIC  -Wall -mtune=core2 -g -O2  -c BetaMix.cpp -o BetaMix.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" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "RcppArmadillo:::CxxFlags()"`   -fPIC  -Wall -mtune=core2 -g -O2  -c MCMC.cpp -o MCMC.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" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c MIMOSA_init.c -o MIMOSA_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" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c betaintegral.c -o betaintegral.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" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "RcppArmadillo:::CxxFlags()"`   -fPIC  -Wall -mtune=core2 -g -O2  -c betaintegralRcpp.cpp -o betaintegralRcpp.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 MIMOSA.so BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -O3 -lm -lstdc++ -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include" -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/MIMOSA.Rcheck/MIMOSA/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘MIMOSA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MIMOSA)

MIMOSA.Rcheck/MIMOSA-Ex.timings:

nameusersystemelapsed
ConstructMIMOSAExpressionSet0.3340.0050.338
MIMOSA-accessors5.5810.1335.715
MIMOSA3.0850.1463.234
MIMOSAExpressionSet0.2740.0000.275
countsTable2.9110.0842.997
fdr3.1180.1323.253
volcanoPlot2.9230.0433.031