rMAT 2.4.2
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/rMAT | | Last Changed Rev: 47925 / Revision: 49923 | | Last Changed Date: 2010-07-06 08:39:53 -0700 (Tue, 06 Jul 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | [ OK ] | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for file 'rMAT/DESCRIPTION' ... OK
* preparing 'rMAT':
* checking DESCRIPTION meta-information ... OK
* cleaning src
make: Nothing to be done for `clean'.
* installing the package to re-build vignettes
* installing *source* package 'rMAT' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
making DLL ...
g++ -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O2 -Wall -c BARFileData.cpp -o BARFileData.o
In file included from BARFileData.cpp:20:
BARFileData.h:29: warning: ignoring #pragma warning
g++ -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O2 -Wall -c BARFileWriter.cpp -o BARFileWriter.o
In file included from BARFileWriter.cpp:20:
BARFileWriter.h:29: warning: ignoring #pragma warning
In file included from BARFileWriter.h:34,
from BARFileWriter.cpp:20:
BARFileData.h:29: warning: ignoring #pragma warning
BARFileWriter.cpp:33: warning: ignoring #pragma warning
g++ -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O2 -Wall -c BARReader.cpp -o BARReader.o
In file included from BARReader.cpp:28:
BARFileData.h:29: warning: ignoring #pragma warning
In file included from E:/biocbld/bbs-2.6-bioc/R/include/R.h:50,
from BARReader.cpp:39:
E:/biocbld/bbs-2.6-bioc/R/include/R_ext/RS.h:43:1: warning: "ERROR" redefined
In file included from c:\rtools211\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/windows.h:52,
from BARFileData.h:30,
from BARReader.cpp:28:
c:\rtools211\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/wingdi.h:313:1: warning: this is the location of the previous definition
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"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O2 -Wall -c BARWriter.cpp -o BARWriter.o
In file included from BARWriter.cpp:30:
BARFileWriter.h:29: warning: ignoring #pragma warning
In file included from BARFileWriter.h:34,
from BARWriter.cpp:30:
BARFileData.h:29: warning: ignoring #pragma warning
In file included from E:/biocbld/bbs-2.6-bioc/R/include/R.h:50,
from BARWriter.cpp:40:
E:/biocbld/bbs-2.6-bioc/R/include/R_ext/RS.h:43:1: warning: "ERROR" redefined
In file included from c:\rtools211\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/windows.h:52,
from BARFileData.h:30,
from BARFileWriter.h:34,
from BARWriter.cpp:30:
c:\rtools211\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/wingdi.h:313:1: warning: this is the location of the previous definition
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"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O2 -Wall -c BPMAPFileData.cpp -o BPMAPFileData.o
In file included from BPMAPFileData.cpp:21:
BPMAPFileData.h:30: warning: ignoring #pragma warning
BPMAPFileData.cpp: In member function 'bool affxbpmap::CBPMAPFileData::ReadDataSection()':
BPMAPFileData.cpp:374: warning: unused variable 'probeIn'
BPMAPFileData.cpp:375: warning: unused variable 'probeOut'
g++ -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O2 -Wall -c BPMAPfunctions.cpp -o BPMAPfunctions.o
In file included from BPMAPfunctions.cpp:9:
BPMAPFileData.h:30: warning: ignoring #pragma warning
In file included from E:/biocbld/bbs-2.6-bioc/R/include/R.h:50,
from BPMAPfunctions.cpp:17:
E:/biocbld/bbs-2.6-bioc/R/include/R_ext/RS.h:43:1: warning: "ERROR" redefined
In file included from c:\rtools211\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/windows.h:52,
from BPMAPFileData.h:31,
from BPMAPfunctions.cpp:9:
c:\rtools211\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/wingdi.h:313:1: warning: this is the location of the previous definition
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O3 -Wall -std=gnu99 -c DeclareAll.c -o DeclareAll.o
g++ -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O2 -Wall -c FileIO.cpp -o FileIO.o
FileIO.cpp:32: warning: ignoring #pragma warning
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"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -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 -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include -O3 -Wall -std=gnu99 -c NormalizeProbes.c -o NormalizeProbes.o
NormalizeProbes.c: In function 'normArray':
NormalizeProbes.c:1052: warning: suggest parentheses around comparison in operand of &
g++ -shared -s -static-libgcc -o rMAT.dll tmp.def BARFileData.o BARFileWriter.o BARReader.o BARWriter.o BPMAPFileData.o BPMAPfunctions.o DeclareAll.o FileIO.o FileWriter.o NormalizeProbes.o -lws2_32 -LC:/gsl/bin -lgsl -lgslcblas -lm -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/tmpdir/Rinst362036874/rMAT/libs
... done
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
rbind, rep.int, table
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Attaching package: 'Biobase'
The following object(s) are masked from 'package:IRanges':
updateObject
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (rMAT)
* creating vignettes ... OK
* cleaning src
make: Nothing to be done for `clean'.
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'rMAT_2.4.2.tar.gz'