gcrma 2.30.0
Z. Wu
| 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/gcrma | | 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 | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/gcrma.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 'gcrma/DESCRIPTION' ... OK
* this is package 'gcrma' version '2.30.0'
* 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 'gcrma' can be installed ... WARNING
Found the following significant warnings:
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
See '/Users/biocbuild/bbs-2.11-bioc/meat/gcrma.Rcheck/00install.out' for details.
* 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 ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
.Call("rma_c_complete", ..., PACKAGE = "affy")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
compute.affinities: no visible binding for global variable
'affinity.spline.coefs'
compute.affinities.nomm: no visible binding for global variable
'affinity.spline.coefs'
compute.affinities2: no visible binding for global variable
'affinity.spline.coefs'
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
bg.adjust.gcrma 54.491 3.966 60.267
gcrma 45.851 3.646 50.892
* 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
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/gcrma.Rcheck/00check.log'
for details.
* installing *source* package 'gcrma' ...
** libs
*** arch - i386
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 baseProfile.c -o baseProfile.o
In file included from baseProfile.c:4:
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
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 computeAffinities.c -o computeAffinities.o
In file included from computeAffinities.c:3:
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
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 postmean.c -o postmean.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 gcrma.so baseProfile.o computeAffinities.o postmean.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/gcrma.Rcheck/gcrma/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'gcrma2.0.Rnw'
** testing if installed package can be loaded
* DONE (gcrma)