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Package 198/553HostnameOS / ArchBUILDCHECKBUILD BIN
gaga 2.2.0
David Rossell
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/gaga
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: gaga
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gaga_2.2.0.tar.gz
StartedAt: 2012-09-24 00:09:28 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:11:12 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 104.1 seconds
RetCode: 0
Status:  OK 
CheckDir: gaga.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/gaga.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 'gaga/DESCRIPTION' ... OK
* this is package 'gaga' version '2.2.0'
* 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 whether package 'gaga' 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
adjustfitNN : f: warning in fitNN(xsim, group = group, trace = FALSE):
  partial argument match of 'group' to 'groups'
adjustfitNN : f: no visible binding for global variable 'x'
adjustfitNN : f: no visible binding for global variable 'group'
adjustfitNN: no visible global function definition for 'mclapply'
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.10-bioc/meat/gaga.Rcheck/gaga/libs/i386/gaga.so':
  Found '___stderrp', possibly from 'stderr' (C)
    Object: 'cstat.o'
  Found '_exit', possibly from 'exit' (C)
    Object: 'cstat.o'
  Found '_printf', possibly from 'printf' (C)
    Objects: 'cseqdesma.o', 'cstat.o'
  Found '_putchar', possibly from 'putchar' (C)
    Objects: 'cseqdesma.o', 'cstat.o'
  Found '_puts', possibly from 'printf' (C), 'puts' (C)
    Objects: 'cseqdesma.o', 'cstat.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* 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 2 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/gaga.Rcheck/00check.log'
for details.

gaga.Rcheck/00install.out:

* installing *source* package 'gaga' ...
** 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 cseqdesma.c -o cseqdesma.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 cstat.c -o cstat.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 gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.10-bioc/meat/gaga.Rcheck/gaga/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'gagamanual.Rnw' 
** testing if installed package can be loaded

* DONE (gaga)

gaga.Rcheck/gaga-Ex.timings:

nameusersystemelapsed
buildPatterns0.0010.0000.001
classpred000
findgenes0.0000.0000.001
fitGG0.2940.0020.297
forwsimDiffExpr3.4350.0223.457
geneclus0.0000.0010.000
parest0.0000.0000.001
powfindgenes0.5720.0010.573
simGG0.0000.0010.000