ArrayExpressHTS 1.2.0
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 55211 / Revision: 59457 | | Last Changed Date: 2011-05-03 06:21:36 -0700 (Tue, 03 May 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | N O T S U P P O R T E D |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘ArrayExpressHTS’ 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 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 ... NOTE
cleanupCluster: no visible global function definition for
‘cleanupClusters’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... 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
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c addXS.c -o addXS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c fltbam.c -o fltbam.o
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c functions.c -o functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c hashtable_itr.c -o hashtable_itr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c hashtable_utility.c -o hashtable_utility.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o -L/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/usrlib/ -lbam -lbcf -lz -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Thu Oct 20 11:41:54 2011 [AEHTS] [TRACE] --> initDefaultEnvironment
* DONE (ArrayExpressHTS)