crlmm 1.2.4
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/crlmm | | Last Changed Rev: 40625 / Revision: 42512 | | Last Changed Date: 2009-07-14 17:21:23 -0700 (Tue, 14 Jul 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | [ OK ] | OK | OK |
* checking for file 'crlmm/DESCRIPTION' ... OK
* preparing 'crlmm':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package ‘crlmm’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCaller.c -o gtypeCaller.o
gtypeCaller.c: In function ‘gtypeCallerPart1’:
gtypeCaller.c:87: warning: unused variable ‘ibv2’
gtypeCaller.c: In function ‘gtypeCallerPart2’:
gtypeCaller.c:310: warning: unused variable ‘ibv2’
gtypeCaller.c:310: warning: unused variable ‘ibv1’
gtypeCaller.c:307: warning: unused variable ‘lenLists’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerNM.c -o gtypeCallerNM.o
gtypeCallerNM.c: In function ‘gtypeCallerPart1nm’:
gtypeCallerNM.c:212: warning: implicit declaration of function ‘mad_median’
gtypeCallerNM.c:87: warning: unused variable ‘ibv2’
gtypeCallerNM.c: In function ‘gtypeCallerPart2nm’:
gtypeCallerNM.c:310: warning: unused variable ‘ibv2’
gtypeCallerNM.c:310: warning: unused variable ‘ibv1’
gtypeCallerNM.c:307: warning: unused variable ‘lenLists’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerNormalNoN.c -o gtypeCallerNormalNoN.o
gtypeCallerNormalNoN.c: In function ‘gtypeCallerPart1NormalNoN’:
gtypeCallerNormalNoN.c:87: warning: unused variable ‘ibv2’
gtypeCallerNormalNoN.c: In function ‘gtypeCallerPart2NormalNoN’:
gtypeCallerNormalNoN.c:292: warning: unused variable ‘ibv2’
gtypeCallerNormalNoN.c:292: warning: unused variable ‘ibv1’
gtypeCallerNormalNoN.c:289: warning: unused variable ‘lenLists’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerTNoN.c -o gtypeCallerTNoN.o
gtypeCallerTNoN.c: In function ‘gtypeCallerPart1TNoN’:
gtypeCallerTNoN.c:87: warning: unused variable ‘ibv2’
gtypeCallerTNoN.c: In function ‘gtypeCallerPart2TNoN’:
gtypeCallerTNoN.c:292: warning: unused variable ‘ibv2’
gtypeCallerTNoN.c:292: warning: unused variable ‘ibv1’
gtypeCallerTNoN.c:289: warning: unused variable ‘lenLists’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c tmp.c -o tmp.o
tmp.c: In function ‘test’:
tmp.c:17: warning: implicit declaration of function ‘genotypeConfidence’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘mad_median’:
utils.c:124: warning: unused variable ‘n_ignore’
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o crlmm.so gtypeCaller.o gtypeCallerNM.o gtypeCallerNormalNoN.o gtypeCallerTNoN.o init.o tmp.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCaller.c -o gtypeCaller.o
gtypeCaller.c: In function ‘gtypeCallerPart1’:
gtypeCaller.c:87: warning: unused variable ‘ibv2’
gtypeCaller.c: In function ‘gtypeCallerPart2’:
gtypeCaller.c:310: warning: unused variable ‘ibv2’
gtypeCaller.c:310: warning: unused variable ‘ibv1’
gtypeCaller.c:307: warning: unused variable ‘lenLists’
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerNM.c -o gtypeCallerNM.o
gtypeCallerNM.c: In function ‘gtypeCallerPart1nm’:
gtypeCallerNM.c:212: warning: implicit declaration of function ‘mad_median’
gtypeCallerNM.c:87: warning: unused variable ‘ibv2’
gtypeCallerNM.c: In function ‘gtypeCallerPart2nm’:
gtypeCallerNM.c:310: warning: unused variable ‘ibv2’
gtypeCallerNM.c:310: warning: unused variable ‘ibv1’
gtypeCallerNM.c:307: warning: unused variable ‘lenLists’
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerNormalNoN.c -o gtypeCallerNormalNoN.o
gtypeCallerNormalNoN.c: In function ‘gtypeCallerPart1NormalNoN’:
gtypeCallerNormalNoN.c:87: warning: unused variable ‘ibv2’
gtypeCallerNormalNoN.c: In function ‘gtypeCallerPart2NormalNoN’:
gtypeCallerNormalNoN.c:292: warning: unused variable ‘ibv2’
gtypeCallerNormalNoN.c:292: warning: unused variable ‘ibv1’
gtypeCallerNormalNoN.c:289: warning: unused variable ‘lenLists’
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerTNoN.c -o gtypeCallerTNoN.o
gtypeCallerTNoN.c: In function ‘gtypeCallerPart1TNoN’:
gtypeCallerTNoN.c:87: warning: unused variable ‘ibv2’
gtypeCallerTNoN.c: In function ‘gtypeCallerPart2TNoN’:
gtypeCallerTNoN.c:292: warning: unused variable ‘ibv2’
gtypeCallerTNoN.c:292: warning: unused variable ‘ibv1’
gtypeCallerTNoN.c:289: warning: unused variable ‘lenLists’
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c tmp.c -o tmp.o
tmp.c: In function ‘test’:
tmp.c:17: warning: implicit declaration of function ‘genotypeConfidence’
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘mad_median’:
utils.c:124: warning: unused variable ‘n_ignore’
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o crlmm.so gtypeCaller.o gtypeCallerNM.o gtypeCallerNormalNoN.o gtypeCallerTNoN.o init.o tmp.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCaller.c -o gtypeCaller.o
gtypeCaller.c: In function ‘gtypeCallerPart1’:
gtypeCaller.c:87: warning: unused variable ‘ibv2’
gtypeCaller.c: In function ‘gtypeCallerPart2’:
gtypeCaller.c:310: warning: unused variable ‘ibv2’
gtypeCaller.c:310: warning: unused variable ‘ibv1’
gtypeCaller.c:307: warning: unused variable ‘lenLists’
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerNM.c -o gtypeCallerNM.o
gtypeCallerNM.c: In function ‘gtypeCallerPart1nm’:
gtypeCallerNM.c:212: warning: implicit declaration of function ‘mad_median’
gtypeCallerNM.c:87: warning: unused variable ‘ibv2’
gtypeCallerNM.c: In function ‘gtypeCallerPart2nm’:
gtypeCallerNM.c:310: warning: unused variable ‘ibv2’
gtypeCallerNM.c:310: warning: unused variable ‘ibv1’
gtypeCallerNM.c:307: warning: unused variable ‘lenLists’
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerNormalNoN.c -o gtypeCallerNormalNoN.o
gtypeCallerNormalNoN.c: In function ‘gtypeCallerPart1NormalNoN’:
gtypeCallerNormalNoN.c:87: warning: unused variable ‘ibv2’
gtypeCallerNormalNoN.c: In function ‘gtypeCallerPart2NormalNoN’:
gtypeCallerNormalNoN.c:292: warning: unused variable ‘ibv2’
gtypeCallerNormalNoN.c:292: warning: unused variable ‘ibv1’
gtypeCallerNormalNoN.c:289: warning: unused variable ‘lenLists’
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerTNoN.c -o gtypeCallerTNoN.o
gtypeCallerTNoN.c: In function ‘gtypeCallerPart1TNoN’:
gtypeCallerTNoN.c:87: warning: unused variable ‘ibv2’
gtypeCallerTNoN.c: In function ‘gtypeCallerPart2TNoN’:
gtypeCallerTNoN.c:292: warning: unused variable ‘ibv2’
gtypeCallerTNoN.c:292: warning: unused variable ‘ibv1’
gtypeCallerTNoN.c:289: warning: unused variable ‘lenLists’
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c tmp.c -o tmp.o
tmp.c: In function ‘test’:
tmp.c:17: warning: implicit declaration of function ‘genotypeConfidence’
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘mad_median’:
utils.c:124: warning: unused variable ‘n_ignore’
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o crlmm.so gtypeCaller.o gtypeCallerNM.o gtypeCallerNormalNoN.o gtypeCallerTNoN.o init.o tmp.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCaller.c -o gtypeCaller.o
gtypeCaller.c: In function ‘gtypeCallerPart1’:
gtypeCaller.c:87: warning: unused variable ‘ibv2’
gtypeCaller.c: In function ‘gtypeCallerPart2’:
gtypeCaller.c:310: warning: unused variable ‘ibv2’
gtypeCaller.c:310: warning: unused variable ‘ibv1’
gtypeCaller.c:307: warning: unused variable ‘lenLists’
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerNM.c -o gtypeCallerNM.o
gtypeCallerNM.c: In function ‘gtypeCallerPart1nm’:
gtypeCallerNM.c:212: warning: implicit declaration of function ‘mad_median’
gtypeCallerNM.c:87: warning: unused variable ‘ibv2’
gtypeCallerNM.c: In function ‘gtypeCallerPart2nm’:
gtypeCallerNM.c:310: warning: unused variable ‘ibv2’
gtypeCallerNM.c:310: warning: unused variable ‘ibv1’
gtypeCallerNM.c:307: warning: unused variable ‘lenLists’
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerNormalNoN.c -o gtypeCallerNormalNoN.o
gtypeCallerNormalNoN.c: In function ‘gtypeCallerPart1NormalNoN’:
gtypeCallerNormalNoN.c:87: warning: unused variable ‘ibv2’
gtypeCallerNormalNoN.c: In function ‘gtypeCallerPart2NormalNoN’:
gtypeCallerNormalNoN.c:292: warning: unused variable ‘ibv2’
gtypeCallerNormalNoN.c:292: warning: unused variable ‘ibv1’
gtypeCallerNormalNoN.c:289: warning: unused variable ‘lenLists’
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCallerTNoN.c -o gtypeCallerTNoN.o
gtypeCallerTNoN.c: In function ‘gtypeCallerPart1TNoN’:
gtypeCallerTNoN.c:87: warning: unused variable ‘ibv2’
gtypeCallerTNoN.c: In function ‘gtypeCallerPart2TNoN’:
gtypeCallerTNoN.c:292: warning: unused variable ‘ibv2’
gtypeCallerTNoN.c:292: warning: unused variable ‘ibv1’
gtypeCallerTNoN.c:289: warning: unused variable ‘lenLists’
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c tmp.c -o tmp.o
tmp.c: In function ‘test’:
tmp.c:17: warning: implicit declaration of function ‘genotypeConfidence’
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘mad_median’:
utils.c:124: warning: unused variable ‘n_ignore’
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o crlmm.so gtypeCaller.o gtypeCallerNM.o gtypeCallerNormalNoN.o gtypeCallerTNoN.o init.o tmp.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> Building/Updating help pages for package 'crlmm'
Formats: text html latex example
celDates text html latex
cnrma text html latex example
computeCopynumber text html latex
crlmm-package text html latex
crlmm text html latex example
crlmmIllumina text html latex example
list.celfiles text html latex example
methods-SnpSet text html latex example
readIdatFiles text html latex example
snprma text html latex example
** building package indices ...
* DONE (crlmm)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'crlmm_1.2.4.tar.gz'