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Package 438/530HostnameOS / ArchBUILDCHECKBUILD BIN
rMAT 3.5.1
Arnaud Droit and Raphael Gottardo
Snapshot Date: 2012-01-18 17:01:22 -0800 (Wed, 18 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rMAT
Last Changed Rev: 60931 / Revision: 62138
Last Changed Date: 2011-11-28 14:34:53 -0800 (Mon, 28 Nov 2011)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS [ OK ]
petty Mac OS X Snow Leopard (10.6.7) / i386  OK  WARNINGS  OK 

Summary

Package: rMAT
Version: 3.5.1
Command: rm -rf rMAT.buildbin-libdir && mkdir rMAT.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe --arch i386 CMD INSTALL --build --no-multiarch --library=rMAT.buildbin-libdir rMAT_3.5.1.tar.gz
StartedAt: 2012-01-19 03:25:38 -0800 (Thu, 19 Jan 2012)
EndedAt: 2012-01-19 03:26:03 -0800 (Thu, 19 Jan 2012)
EllapsedTime: 25.0 seconds
RetCode: 0
Status:  OK  
PackageFile: rMAT_3.5.1.zip
PackageFileSize: 885.1 KiB

Command output

* installing *source* package 'rMAT' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++  -I"E:/biocbld/bbs-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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"E:/biocbld/bbs-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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"E:/biocbld/bbs-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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 E:/biocbld/bbs-2.10-bioc/R/include/R.h:44:0,
                 from BARReader.cpp:39:
E:/biocbld/bbs-2.10-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools215\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-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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 E:/biocbld/bbs-2.10-bioc/R/include/R.h:44:0,
                 from BARWriter.cpp:40:
E:/biocbld/bbs-2.10-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools215\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-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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"E:/biocbld/bbs-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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 E:/biocbld/bbs-2.10-bioc/R/include/R.h:44:0,
                 from BPMAPfunctions.cpp:17:
E:/biocbld/bbs-2.10-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools215\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-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DeclareAll.c -o DeclareAll.o
g++  -I"E:/biocbld/bbs-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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"E:/biocbld/bbs-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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"E:/biocbld/bbs-2.10-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/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/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -lws2_32 -LC:/GSL/i386/lib -lgsl -lgslcblas -lm -LE:/biocbld/bbs-2.10-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/rMAT.buildbin-libdir/rMAT/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'lapply' when loading 'IRanges'
Warning: replacing previous import 'combine' when loading 'Biobase'
** help
*** installing help indices
** building package indices
** installing vignettes
   'rMAT.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'lapply' when loading 'IRanges'
Warning: replacing previous import 'combine' when loading 'Biobase'
Warning: Functions for exporting methods must have been made generic, explicitly or implicitly; not true when loading 'rMAT' for 'summary'
* MD5 sums
packaged installation of 'rMAT' as rMAT_3.5.1.zip

* DONE (rMAT)