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BioC 2.12: CHECK report for DNAcopy on george2

This page was generated on 2013-10-09 09:37:14 -0700 (Wed, 09 Oct 2013).

Package 185/671HostnameOS / ArchBUILDCHECKBUILD BIN
DNAcopy 1.34.0
Venkatraman E. Seshan
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DNAcopy
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: DNAcopy
Version: 1.34.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.34.0.tar.gz
StartedAt: 2013-10-09 01:24:11 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:24:49 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 38.1 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/DNAcopy.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.34.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DNAcopy’ can be installed ... [6s/6s] 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 ... 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 ... [7s/7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘redundancy,20090610,segment.R’ [1s/1s]
 [1s/1s] 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

DNAcopy.Rcheck/00install.out:

* installing *source* package ‘DNAcopy’ ...
** libs
gfortran   -fpic  -g -O2  -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function ‘wtmaxo’:
cbsWtstats.f:283:0: warning: ‘tmaxj’ may be used uninitialized in this function [-Wuninitialized]
cbsWtstats.f:282:0: warning: ‘tmaxi’ may be used uninitialized in this function [-Wuninitialized]
gfortran   -fpic  -g -O2  -Wall -c cbststats.f -o cbststats.o
cbststats.f: In function ‘tmaxo’:
cbststats.f:258:0: warning: ‘sxmxi’ may be used uninitialized in this function [-Wuninitialized]
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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c flchoose.c -o flchoose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fphyper.c -o fphyper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -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-2.12-bioc/R/include -DNDEBUG  -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/lib -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 -lquadmath -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
** installing vignettes
** testing if installed package can be loaded
* DONE (DNAcopy)

DNAcopy.Rcheck/DNAcopy-Ex.timings:

nameusersystemelapsed
CNA0.0680.0080.075
exon.segment0.2040.0080.213
plot.DNAcopy1.3200.0121.431
plotSample0.9680.0041.038
segment2.1080.0162.127
segments.p0.1320.0040.135
segments.summary0.1680.0000.171
smooth.CNA0.0520.0040.056
subset.CNA0.0400.0000.037
zoomIntoRegion0.9280.0000.930