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 |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.5-bioc/meat/rMAT.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rMAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rMAT' version '2.2.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rMAT' 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 name space can be loaded with stated dependencies ... 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 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* 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)