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Package 314/553HostnameOS / ArchBUILDCHECKBUILD BIN
maanova 1.26.0
Keith Sheppard
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/maanova
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: maanova
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maanova_1.26.0.tar.gz
StartedAt: 2012-09-24 00:46:48 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:47:53 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 64.3 seconds
RetCode: 0
Status:  OK 
CheckDir: maanova.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/maanova.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'maanova/DESCRIPTION' ... OK
* this is package 'maanova' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'maanova' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
  argument match of 'r' to 'red'
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
  argument match of 'g' to 'green'
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
  argument match of 'b' to 'blue'
* 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 for portable compilation flags in Makevars ... 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' ... NOTE
The following files should probably not be installed:
  'MPI.tex', 'Rtour.tex', 'abf1.tex', 'algorithm.tex', 'camda.tex',
  'faq.tex', 'intro.tex', 'paigen.tex', 'prepfile.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/maanova.Rcheck/00check.log'
for details.

maanova.Rcheck/00install.out:

* installing *source* package 'maanova' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c makeratio.c -o makeratio.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c masvd.c -o masvd.o
masvd.c:114:2: warning: "/*" within comment
masvd.c:154:1: warning: "/*" within comment
masvd.c:161:5: warning: "/*" within comment
masvd.c:165:2: warning: "/*" within comment
masvd.c:189:2: warning: "/*" within comment
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c shift.c -o shift.o
shift.c: In function 'shift':
shift.c:27: warning: unused variable 'k'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c util.c -o util.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o maanova.so makeratio.o masvd.o shift.o util.o -L/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/i386 -lRblas -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.10-bioc/meat/maanova.Rcheck/maanova/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'maanova.Rnw' 
** testing if installed package can be loaded

* DONE (maanova)

maanova.Rcheck/maanova-Ex.timings:

nameusersystemelapsed
PairContrast0.0310.0040.036
Rmaanova.version0.0060.0020.009
abf10.0090.0010.010
adjPval0.0120.0020.013
arrayview0.0000.0000.001
consensus0.0090.0010.011
dyeswapfilter000
fill.missing0.3080.0200.329
fitmaanova0.0090.0010.011
fom0.0090.0010.010
geneprofile0.0100.0010.010
gridcheck0.0010.0000.000
kidney0.0920.0090.101
maanova-internal0.0020.0010.003
macluster0.0090.0010.011
matest0.0100.0010.010
read.madata0.0010.0010.000
resiplot0.0110.0010.013
riplot0.0000.0010.000
subset.madata0.0880.0080.096
summarytable0.0090.0010.010
transform.madata0.0900.0090.099
varplot0.0090.0010.011
volcano0.0000.0000.001
write.madata0.0090.0010.011