Package: DEGseq

Version: 1.13.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DEGseq_1.13.1.tar.gz

StartedAt: 2013-01-16 02:03:13 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:04:11 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 57.3 seconds

RetCode: 0

Status:  OK

CheckDir: DEGseq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/DEGseq.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 ‘DEGseq/DESCRIPTION’ ... OK
* this is package ‘DEGseq’ version ‘1.13.1’
* 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 ‘DEGseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
    libs      1.1Mb
* 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
FindDiff_FET: warning in matrix(c(o1, o2, count1 - o1, count2 - o2), nr
  = 2): partial argument match of 'nr' to 'nrow'
png_new: warning in png(file = file, units = "px", width = 480, height
  = 480): partial argument match of 'file' to 'filename'
AVal,lanePair: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
AVal,lanePair: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
MVal,lanePair: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
MVal,lanePair: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
* 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 ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/DEGseq.Rcheck/DEGseq/libs/DEGseq.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘getGeneExp.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
Examples with CPU or elapsed time > 5s
           user system elapsed
samWrapper 7.02  0.116   7.146
* 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/DEGseq.Rcheck/00check.log’
for details.

* installing *source* package ‘DEGseq’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c getGeneExp.cpp -o getGeneExp.o
g++ -shared -L/usr/local/lib64 -o DEGseq.so getGeneExp.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/DEGseq.Rcheck/DEGseq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘DEGseq.Rnw’ 
** testing if installed package can be loaded

* DONE (DEGseq)

name	user	system	elapsed
DEGexp	2.296	0.016	2.349
DEGexp2	4.588	0.048	4.645
DEGseq	0.528	0.020	0.549
getGeneExp	0.172	0.008	0.182
readGeneExp	0.064	0.004	0.067
samWrapper	7.020	0.116	7.146