Package: CGEN

Version: 2.0.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CGEN_2.0.1.tar.gz

StartedAt: 2013-01-16 01:20:03 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:21:59 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 115.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CGEN.Rcheck

Warnings: 2

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/CGEN.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 ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘2.0.1’
* 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 ‘CGEN’ 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 ... OK
* 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 ... WARNING
‘library’ or ‘require’ call not declared from: ‘cluster’
* 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 ... WARNING
File ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/CGEN.Rcheck/CGEN/libs/CGEN.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘ccl.o’, ‘hcl.o’
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘Additive.o’, ‘CML.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘Additive.o’, ‘CML.o’, ‘ccl.o’, ‘hcl.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
getMatchedSets 29.589    0.3  29.904
snp.matched    22.009    0.0  22.012
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘cluster’
* 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 were 2 warnings.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/CGEN.Rcheck/00check.log’
for details.

* installing *source* package ‘CGEN’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Additive.c -o Additive.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c CML.c -o CML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ccl.c -o ccl.o
gfortran   -fpic  -g -O2  -c csclust.f -o csclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c fsclust.c -o fsclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hcl.c -o hcl.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pmatch.c -o pmatch.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -lgfortran -lm -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/CGEN.Rcheck/CGEN/libs
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘vignette.Rnw’ 
** testing if installed package can be loaded

* DONE (CGEN)

name	user	system	elapsed
LocusMapData	0.036	0.004	0.044
QQ.plot	0.028	0.004	0.029
SNPdata	0.080	0.000	0.078
Xdata	0.028	0.000	0.028
additive.test	1.288	0.004	1.295
chromosome.plot	0.236	0.004	0.242
getMatchedSets	29.589	0.300	29.904
getSummary	0.020	0.000	0.019
getWaldTest	0.012	0.004	0.015
printEffects	0.204	0.004	0.205
recode.geno	0.021	0.000	0.022
snp.effects	0.192	0.004	0.196
snp.effects.plot	0.788	0.008	0.796
snp.list	0.008	0.000	0.010
snp.logistic	0.352	0.000	0.351
snp.matched	22.009	0.000	22.012
snp.scan.logistic	0.028	0.000	0.029