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Package 127/462HostnameOS / ArchBUILDCHECKBUILD BIN
DNAcopy 1.27.0
Venkatraman E. Seshan
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DNAcopy
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DNAcopy
Version: 1.27.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.27.0.tar.gz
StartedAt: 2011-05-09 12:14:43 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:15:05 -0700 (Mon, 09 May 2011)
EllapsedTime: 22.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/DNAcopy.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.27.0’
* 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

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: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)

DNAcopy.Rcheck/DNAcopy-Ex.timings:

nameusersystemelapsed
CNA0.0200.0000.021
exon.segment0.1640.0000.163
plot.DNAcopy0.9520.0040.959
plotSample0.8120.0040.817
segment1.8160.0041.817
segments.p0.0880.0000.087
segments.summary0.0880.0000.091
smooth.CNA0.0680.0000.066
subset.CNA0.0080.0000.007
zoomIntoRegion0.8280.0040.832