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Package 288/353HostnameOS / ArchBUILDCHECKBUILD BIN
rMAT 2.2.0
Arnaud Droit and Raphael Gottardo
Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/rMAT
Last Changed Rev: 42684 / Revision: 43539
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 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 
Package: rMAT
Version: 2.2.0
Command: /home/biocbuild/bbs-2.5-bioc/R/bin/R CMD build rMAT
StartedAt: 2009-12-14 02:31:36 -0800 (Mon, 14 Dec 2009)
EndedAt: 2009-12-14 02:31:53 -0800 (Mon, 14 Dec 2009)
EllapsedTime: 17.5 seconds
RetCode: 0
Status: OK
PackageFile: rMAT_2.2.0.tar.gz
PackageFileSize: 484.1 KiB

Command output

* checking for file 'rMAT/DESCRIPTION' ... OK
* preparing 'rMAT':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running cleanup
* installing the package to re-build vignettes
* installing *source* package ‘rMAT’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c BARFileData.cpp -o BARFileData.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c BARFileWriter.cpp -o BARFileWriter.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c BARReader.cpp -o BARReader.o
BARReader.cpp: In function ‘SEXPREC* Parser(SEXPREC*)’:
BARReader.cpp:258: warning: unused variable ‘buf’
BARReader.cpp: In function ‘SEXPREC* ParseMATBar(SEXPREC*)’:
BARReader.cpp:472: warning: unused variable ‘regionR’
BARReader.cpp:473: warning: unused variable ‘p_region’
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c BARWriter.cpp -o BARWriter.o
BARWriter.cpp: In function ‘SEXPREC* WriteBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
BARWriter.cpp:87: warning: unused variable ‘signal2Length’
BARWriter.cpp:90: warning: unused variable ‘lengthList’
BARWriter.cpp:91: warning: unused variable ‘curListPtr’
BARWriter.cpp:91: warning: unused variable ‘startListPtr’
BARWriter.cpp:92: warning: unused variable ‘curChromosome’
BARWriter.cpp:93: warning: unused variable ‘i’
BARWriter.cpp: In function ‘SEXPREC* WriteNormalizedBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
BARWriter.cpp:271: warning: unused variable ‘addPos’
BARWriter.cpp: In function ‘SEXPREC* testBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
BARWriter.cpp:78: warning: control reaches end of non-void function
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c BPMAPFileData.cpp -o BPMAPFileData.o
BPMAPFileData.cpp: In member function ‘bool affxbpmap::CBPMAPFileData::ReadDataSection()’:
BPMAPFileData.cpp:379: warning: unused variable ‘hitSize’
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c BPMAPfunctions.cpp -o BPMAPfunctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c DeclareAll.c -o DeclareAll.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c FileIO.cpp -o FileIO.o
FileIO.cpp: In function ‘float MmGetFloat_I(float*)’:
FileIO.cpp:362: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function ‘void MmSetFloat_I(float*, float)’:
FileIO.cpp:367: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function ‘float MmGetFloat_N(float*)’:
FileIO.cpp:373: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function ‘void MmSetFloat_N(float*, float)’:
FileIO.cpp:378: warning: dereferencing type-punned pointer will break strict-aliasing rules
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c FileWriter.cpp -o FileWriter.o
FileWriter.cpp: In function ‘void WriteFloat_I(std::ofstream&, float)’:
FileWriter.cpp:108: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileWriter.cpp: In function ‘void WriteFloat_N(std::ofstream&, float)’:
FileWriter.cpp:113: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c NormalizeProbes.c -o NormalizeProbes.o
g++ -shared -L/usr/local/lib64 -o rMAT.so BARFileData.o BARFileWriter.o BARReader.o BARWriter.o BPMAPFileData.o BPMAPfunctions.o DeclareAll.o FileIO.o FileWriter.o NormalizeProbes.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.5-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 Map,
	 cbind,
	 mapply,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rbind,
	 rep.int,
	 table 

** help
*** installing help indices
** building package indices ...
* DONE (rMAT)
* creating vignettes ... OK
* cleaning src
make: Nothing to be done for `clean'.
* running cleanup
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'rMAT_2.2.0.tar.gz'