BioC 2.9: CHECK report for DNAcopy on wilson2

Package: DNAcopy

Version: 1.27.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.27.1.tar.gz

StartedAt: 2011-07-07 00:18:47 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 00:19:09 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 22.2 seconds

RetCode: 0

Status: OK

CheckDir: DNAcopy.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/DNAcopy.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNAcopy/DESCRIPTION’ ... OK
* this is package ‘DNAcopy’ version ‘1.27.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘DNAcopy’ 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘redundancy,20090610,segment.R’
 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

* installing *source* package ‘DNAcopy’ ...
** libs
gfortran   -fpic  -g -O2 -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function ‘wtmaxo’:
cbsWtstats.f:17:0: warning: ‘tmaxi’ may be used uninitialized in this function
cbsWtstats.f:17:0: warning: ‘tmaxj’ may be used uninitialized in this function
gfortran   -fpic  -g -O2 -Wall -c cbststats.f -o cbststats.o
cbststats.f: In function ‘tmaxo’:
cbststats.f:11:0: warning: ‘sxmxi’ may be used uninitialized in this function
gfortran   -fpic  -g -O2 -Wall -c changepoints-wtd.f -o changepoints-wtd.o
gfortran   -fpic  -g -O2 -Wall -c changepoints.f -o changepoints.o
gfortran   -fpic  -g -O2 -Wall -c esegment.f -o esegment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c flchoose.c -o flchoose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c fphyper.c -o fphyper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c fpnorm.c -o fpnorm.o
gfortran   -fpic  -g -O2 -Wall -c getbdry.f -o getbdry.o
gfortran   -fpic  -g -O2 -Wall -c prune.f -o prune.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rshared.c -o rshared.o
gfortran   -fpic  -g -O2 -Wall -c segmentp.f -o segmentp.o
gfortran   -fpic  -g -O2 -Wall -c smoothCNA.f -o smoothCNA.o
gfortran   -fpic  -g -O2 -Wall -c tailprobs.f -o tailprobs.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/DNAcopy.Rcheck/DNAcopy/libs
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘DNAcopy.Rnw’ 
** testing if installed package can be loaded

* DONE (DNAcopy)

name	user	system	elapsed
CNA	0.020	0.004	0.021
exon.segment	0.164	0.000	0.164
plot.DNAcopy	1.024	0.000	1.023
plotSample	0.876	0.004	0.879
segment	1.736	0.004	1.745
segments.p	0.088	0.000	0.089
segments.summary	0.096	0.000	0.095
smooth.CNA	0.064	0.000	0.063
subset.CNA	0.012	0.000	0.010
zoomIntoRegion	0.832	0.000	0.839

Summary

Command output