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Package 226/631HostnameOS / ArchBUILDCHECKBUILD BIN
gaga 2.5.0
David Rossell
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gaga
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: gaga
Version: 2.5.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings gaga_2.5.0.tar.gz
StartedAt: 2013-01-16 02:38:21 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 02:40:20 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 119.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: gaga.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaga/DESCRIPTION’ ... OK
* this is package ‘gaga’ version ‘2.5.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ‘gaga’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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", B = B, trace =
  FALSE): partial argument match of 'group' to 'groups'
* 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 ... WARNING
File ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck/gaga/libs/gaga.so’:
  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’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘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 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck/00check.log’
for details.

gaga.Rcheck/00install.out:

* installing *source* package ‘gaga’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cseqdesma.c -o cseqdesma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cstat.c -o cstat.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o gaga.so cseqdesma.o cstat.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck/gaga/libs
** 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
buildPatterns0.0040.0040.006
classpred0.0120.0000.010
findgenes0.0120.0000.012
fitGG0.2320.0120.242
forwsimDiffExpr3.2160.0083.226
geneclus0.0040.0040.009
parest0.0040.0040.008
powfindgenes0.5560.0000.554
simGG0.0080.0000.008