rMAT 3.4.1
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2012-02-28 18:21:37 -0800 (Tue, 28 Feb 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/rMAT | | Last Changed Rev: 60373 / Revision: 63268 | | Last Changed Date: 2011-11-15 17:44:53 -0800 (Tue, 15 Nov 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* installing *source* package 'rMAT' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O2 -Wall -mtune=core2 -c BARFileData.cpp -o BARFileData.o
In file included from BARFileData.cpp:20:0:
BARFileData.h:29:0: warning: ignoring #pragma warning
g++ -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O2 -Wall -mtune=core2 -c BARFileWriter.cpp -o BARFileWriter.o
In file included from BARFileWriter.cpp:20:0:
BARFileWriter.h:29:0: warning: ignoring #pragma warning
In file included from BARFileWriter.h:34:0,
from BARFileWriter.cpp:20:
BARFileData.h:29:0: warning: ignoring #pragma warning
BARFileWriter.cpp:33:0: warning: ignoring #pragma warning
g++ -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O2 -Wall -mtune=core2 -c BARReader.cpp -o BARReader.o
In file included from BARReader.cpp:28:0:
BARFileData.h:29:0: warning: ignoring #pragma warning
In file included from D:/biocbld/bbs-2.9-bioc/R/include/R.h:44:0,
from BARReader.cpp:39:
D:/biocbld/bbs-2.9-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
BARReader.cpp: In function 'SEXPREC* Parser(SEXPREC*)':
BARReader.cpp:258:18: warning: unused variable 'buf'
BARReader.cpp: In function 'SEXPREC* ParseMATBar(SEXPREC*)':
BARReader.cpp:472:42: warning: unused variable 'regionR'
BARReader.cpp:473:49: warning: unused variable 'p_region'
g++ -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O2 -Wall -mtune=core2 -c BARWriter.cpp -o BARWriter.o
In file included from BARWriter.cpp:30:0:
BARFileWriter.h:29:0: warning: ignoring #pragma warning
In file included from BARFileWriter.h:34:0,
from BARWriter.cpp:30:
BARFileData.h:29:0: warning: ignoring #pragma warning
In file included from D:/biocbld/bbs-2.9-bioc/R/include/R.h:44:0,
from BARWriter.cpp:40:
D:/biocbld/bbs-2.9-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
BARWriter.cpp: In function 'SEXPREC* testBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
BARWriter.cpp:78:3: warning: no return statement in function returning non-void
BARWriter.cpp: In function 'SEXPREC* WriteBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
BARWriter.cpp:87:9: warning: unused variable 'signal2Length'
BARWriter.cpp:90:10: warning: unused variable 'lengthList'
BARWriter.cpp:91:9: warning: unused variable 'curListPtr'
BARWriter.cpp:91:25: warning: unused variable 'startListPtr'
BARWriter.cpp:92:9: warning: unused variable 'curChromosome'
BARWriter.cpp:93:9: warning: unused variable 'i'
BARWriter.cpp: In function 'SEXPREC* WriteNormalizedBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
BARWriter.cpp:271:6: warning: unused variable 'addPos'
g++ -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O2 -Wall -mtune=core2 -c BPMAPFileData.cpp -o BPMAPFileData.o
In file included from BPMAPFileData.cpp:21:0:
BPMAPFileData.h:30:0: warning: ignoring #pragma warning
BPMAPFileData.cpp: In member function 'bool affxbpmap::CBPMAPFileData::ReadDataSection()':
BPMAPFileData.cpp:374:51: warning: unused variable 'probeIn'
BPMAPFileData.cpp:375:28: warning: unused variable 'probeOut'
g++ -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O2 -Wall -mtune=core2 -c BPMAPfunctions.cpp -o BPMAPfunctions.o
In file included from BPMAPfunctions.cpp:9:0:
BPMAPFileData.h:30:0: warning: ignoring #pragma warning
In file included from D:/biocbld/bbs-2.9-bioc/R/include/R.h:44:0,
from BPMAPfunctions.cpp:17:
D:/biocbld/bbs-2.9-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
gcc -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DeclareAll.c -o DeclareAll.o
g++ -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O2 -Wall -mtune=core2 -c FileIO.cpp -o FileIO.o
FileIO.cpp:32:0: warning: ignoring #pragma warning
FileIO.cpp: In function 'float MmGetFloat_I(float*)':
FileIO.cpp:362:22: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function 'void MmSetFloat_I(float*, float)':
FileIO.cpp:367:19: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function 'float MmGetFloat_N(float*)':
FileIO.cpp:373:22: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function 'void MmSetFloat_N(float*, float)':
FileIO.cpp:378:38: warning: dereferencing type-punned pointer will break strict-aliasing rules
g++ -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O2 -Wall -mtune=core2 -c FileWriter.cpp -o FileWriter.o
FileWriter.cpp: In function 'void WriteFloat_I(std::ofstream&, float)':
FileWriter.cpp:108:42: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileWriter.cpp: In function 'void WriteFloat_N(std::ofstream&, float)':
FileWriter.cpp:113:42: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -I"D:/biocbld/bbs-2.9-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -I"d:/RCompile/CRANpkg/extralibs/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c NormalizeProbes.c -o NormalizeProbes.o
NormalizeProbes.c: In function 'NormalizeProbes':
NormalizeProbes.c:91:13: warning: unused variable 'j'
NormalizeProbes.c: In function 'normArray':
NormalizeProbes.c:1030:9: 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 -Ld:/RCompile/CRANpkg/extralibs/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs/local/lib -lws2_32 -LC:/GSL/i386/lib -lgsl -lgslcblas -lm -LD:/biocbld/bbs-2.9-bioc/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/rMAT.buildbin-libdir/rMAT/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'rMAT.Rnw'
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rMAT' as rMAT_3.4.1.zip
* DONE (rMAT)