rMAT 3.0.0
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/rMAT | | Last Changed Rev: 50293 / Revision: 54281 | | Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010) |
| lamb2 | Linux (openSUSE 11.2) / 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 |
* installing *source* package 'rMAT' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -I"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O2 -Wall -c BARFileData.cpp -o BARFileData.o
In file included from BARFileData.cpp:20:0:
BARFileData.h:29:0: warning: ignoring #pragma warning
g++ -I"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O2 -Wall -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"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O2 -Wall -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 E:/biocbld/bbs-2.7-bioc/R/include/R.h:44:0,
from BARReader.cpp:39:
E:/biocbld/bbs-2.7-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools212\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"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O2 -Wall -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 E:/biocbld/bbs-2.7-bioc/R/include/R.h:44:0,
from BARWriter.cpp:40:
E:/biocbld/bbs-2.7-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools212\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"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O2 -Wall -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"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O2 -Wall -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 E:/biocbld/bbs-2.7-bioc/R/include/R.h:44:0,
from BPMAPfunctions.cpp:17:
E:/biocbld/bbs-2.7-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools212\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O3 -Wall -std=gnu99 -c DeclareAll.c -o DeclareAll.o
g++ -I"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O2 -Wall -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"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/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:108:42: 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"E:/biocbld/bbs-2.7-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/gsl/include -O3 -Wall -std=gnu99 -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 -lws2_32 -LC:/gsl/bin -lgsl -lgslcblas -lm -LE:/biocbld/bbs-2.7-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-bioc/meat/rMAT.buildbin-libdir/rMAT/libs/i386
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, 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
* MD5 sums
packaged installation of 'rMAT' as rMAT_3.0.0.zip
* DONE (rMAT)