DNAcopy 1.22.1
Venkatraman E. Seshan
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/DNAcopy | | Last Changed Rev: 46873 / Revision: 49923 | | Last Changed Date: 2010-05-14 13:34:58 -0700 (Fri, 14 May 2010) |
| wilson1 | Linux (openSUSE 11.1) / 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 |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/DNAcopy.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DNAcopy/DESCRIPTION' ... OK
* this is package 'DNAcopy' version '1.22.1'
* 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 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
Running ‘redundancy,20090610,segment.R’
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* 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/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -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/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -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/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -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/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -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-2.6-bioc/meat/DNAcopy.Rcheck/DNAcopy/libs/i386
*** arch - ppc
gfortran -arch ppc -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 ppc -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 ppc -fPIC -g -O2 -Wall -pedantic -c changepoints-wtd.f -o changepoints-wtd.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c changepoints.f -o changepoints.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c esegment.f -o esegment.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c flchoose.c -o flchoose.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c fphyper.c -o fphyper.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c fpnorm.c -o fpnorm.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c getbdry.f -o getbdry.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c prune.f -o prune.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c rshared.c -o rshared.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c segmentp.f -o segmentp.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c smoothCNA.f -o smoothCNA.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c tailprobs.f -o tailprobs.o
gcc -arch ppc -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 -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/DNAcopy.Rcheck/DNAcopy/libs/ppc
*** arch - x86_64
gfortran -arch x86_64 -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 x86_64 -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 x86_64 -fPIC -g -O2 -Wall -pedantic -c changepoints-wtd.f -o changepoints-wtd.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c changepoints.f -o changepoints.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c esegment.f -o esegment.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c flchoose.c -o flchoose.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c fphyper.c -o fphyper.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c fpnorm.c -o fpnorm.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c getbdry.f -o getbdry.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c prune.f -o prune.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c rshared.c -o rshared.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c segmentp.f -o segmentp.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c smoothCNA.f -o smoothCNA.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c tailprobs.f -o tailprobs.o
gcc -arch x86_64 -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-2.6-bioc/meat/DNAcopy.Rcheck/DNAcopy/libs/x86_64
** R
** data
** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (DNAcopy)