Package: DEDS

Version: 1.30.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings DEDS_1.30.0.tar.gz

StartedAt: 2012-09-24 00:22:53 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:23:28 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 35.3 seconds

RetCode: 0

Status:  OK

CheckDir: DEDS.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/DEDS.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEDS/DESCRIPTION’ ... OK
* this is package ‘DEDS’ version ‘1.30.0’
* 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 ‘DEDS’ 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
deds.stat.linkC: warning in matrix(res$t, byrow = FALSE, nc = newX$nT):
  partial argument match of 'nc' to 'ncol'
sam.multiclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.multiclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
sam.oneclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.oneclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
sam.twoclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.twoclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
* checking Rd files ... NOTE
prepare_Rd: comp.fdr.Rd:52-54: Dropping empty section \details
prepare_Rd: deds.pval.Rd:65-68: Dropping empty section \examples
prepare_Rd: hist.DEDS.Rd:47-50: Dropping empty section \examples
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/DEDS.Rcheck/00check.log’
for details.

* installing *source* package ‘DEDS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c deds.c -o deds.o
deds.c: In function ‘type2stat’:
deds.c:451:21: warning: ‘test’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c distance.c -o distance.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c input.c -o input.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c manip.c -o manip.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c random.c -o random.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sampling.c -o sampling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c stat_fun.c -o stat_fun.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DEDS.so deds.o distance.o input.o manip.o random.o sampling.o stat_fun.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/DEDS.Rcheck/DEDS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘DEDS.rnw’ 
** testing if installed package can be loaded

* DONE (DEDS)

name	user	system	elapsed
aggregateFun	0.012	0.000	0.014
comp.B	0.004	0.000	0.004
comp.F	0.316	0.000	0.331
comp.FC	0.004	0.000	0.005
comp.SAM	1.296	0.020	1.317
comp.adjp	0.012	0.000	0.009
comp.ebayes	0.004	0.000	0.003
comp.fdr	0.016	0.000	0.018
comp.modF	0.000	0.000	0.002
comp.modt	0.004	0.000	0.003
comp.stat	0.008	0.000	0.005
comp.t	0.020	0.000	0.019
comp.unadjp	0.008	0.000	0.009
deds.chooseTest	5.408	0.004	5.415
deds.genExtra	0.000	0.004	0.001
deds.stat	4.148	0.004	4.154
deds.stat.linkC	0.024	0.004	0.027
pairs.DEDS	0.128	0.008	0.133
qqnorm.DEDS	0.040	0.008	0.048
topgenes	0.032	0.000	0.031