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Package 169/609HostnameOS / ArchBUILDCHECKBUILD BIN
DNAcopy 1.32.0
Venkatraman E. Seshan
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/DNAcopy
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: DNAcopy
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DNAcopy_1.32.0.tar.gz
StartedAt: 2013-03-24 23:17:53 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:18:26 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 33.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/DNAcopy.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DNAcopy/DESCRIPTION' ... OK
* this is package 'DNAcopy' version '1.32.0'
* 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 '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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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
*** arch - i386
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function 'wtmaxo':
cbsWtstats.f:17: warning: 'tmaxj' may be used uninitialized in this function
cbsWtstats.f:17: warning: 'tmaxi' may be used uninitialized in this function
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c cbststats.f -o cbststats.o
cbststats.f: In function 'tmaxo':
cbststats.f:11: warning: 'sxmxi' may be used uninitialized in this function
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c changepoints-wtd.f -o changepoints-wtd.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c changepoints.f -o changepoints.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c esegment.f -o esegment.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c flchoose.c -o flchoose.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fphyper.c -o fphyper.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fpnorm.c -o fpnorm.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c getbdry.f -o getbdry.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c prune.f -o prune.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c rshared.c -o rshared.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c segmentp.f -o segmentp.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c smoothCNA.f -o smoothCNA.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c tailprobs.f -o tailprobs.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/DNAcopy.Rcheck/DNAcopy/libs/i386
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DNAcopy.Rnw' 
** testing if installed package can be loaded

* DONE (DNAcopy)

DNAcopy.Rcheck/DNAcopy-Ex.timings:

nameusersystemelapsed
CNA0.0310.0080.040
exon.segment0.1440.0010.145
plot.DNAcopy1.3340.0701.413
plotSample1.1680.0571.236
segment2.4300.1232.573
segments.p0.1230.0050.129
segments.summary0.1180.0080.127
smooth.CNA0.0510.0380.097
subset.CNA0.0100.0030.013
zoomIntoRegion1.1280.0441.182