rMAT 3.1.4
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2011-04-11 11:17:10 -0700 (Mon, 11 Apr 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rMAT | | Last Changed Rev: 54691 / Revision: 54695 | | Last Changed Date: 2011-04-11 09:10:16 -0700 (Mon, 11 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | [ ERROR ] | skipped | skipped |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* checking for file 'rMAT/DESCRIPTION' ... OK
* preparing 'rMAT':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
-----------------------------------
* installing *source* package 'rMAT' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/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 D:/biocbld/BBS-2˜1.8-B/R/include/R.h:44:0,
from BARReader.cpp:39:
D:/biocbld/BBS-2˜1.8-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools213/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: 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'
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/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 D:/biocbld/BBS-2˜1.8-B/R/include/R.h:44:0,
from BARWriter.cpp:40:
D:/biocbld/BBS-2˜1.8-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools213/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: 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'
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/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'
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/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 D:/biocbld/BBS-2˜1.8-B/R/include/R.h:44:0,
from BPMAPfunctions.cpp:17:
D:/biocbld/BBS-2˜1.8-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools213/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: note: this is the location of the previous definition
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/include -O2 -Wall -std=gnu99 -c DeclareAll.c -o DeclareAll.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -Ic:/Rtools212/GSL64/include -O2 -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 '&'
x86_64-w64-mingw32-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:/Rtools212/GSL64/lib -lgsl -lgslcblas -lm -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
NormalizeProbes.o:NormalizeProbes.c:(.text+0x0): multiple definition of `_Exit'
DeclareAll.o:DeclareAll.c:(.text+0x0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x10): multiple definition of `llabs'
DeclareAll.o:DeclareAll.c:(.text+0x10): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x30): multiple definition of `atoll'
DeclareAll.o:DeclareAll.c:(.text+0x30): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x50): multiple definition of `lltoa'
DeclareAll.o:DeclareAll.c:(.text+0x50): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x70): multiple definition of `ulltoa'
DeclareAll.o:DeclareAll.c:(.text+0x70): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x90): multiple definition of `wtoll'
DeclareAll.o:DeclareAll.c:(.text+0x90): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0xb0): multiple definition of `lltow'
DeclareAll.o:DeclareAll.c:(.text+0xb0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0xd0): multiple definition of `ulltow'
DeclareAll.o:DeclareAll.c:(.text+0xd0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0xf0): multiple definition of `vsnprintf'
DeclareAll.o:DeclareAll.c:(.text+0xf0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x110): multiple definition of `vsnwprintf'
DeclareAll.o:DeclareAll.c:(.text+0x110): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x130): multiple definition of `__fpclassifyl'
DeclareAll.o:DeclareAll.c:(.text+0x130): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x150): multiple definition of `__fpclassify'
DeclareAll.o:DeclareAll.c:(.text+0x150): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x170): multiple definition of `__fpclassifyf'
DeclareAll.o:DeclareAll.c:(.text+0x170): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x190): multiple definition of `__isnan'
DeclareAll.o:DeclareAll.c:(.text+0x190): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x1c0): multiple definition of `__isnanf'
DeclareAll.o:DeclareAll.c:(.text+0x1c0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x1f0): multiple definition of `__isnanl'
DeclareAll.o:DeclareAll.c:(.text+0x1f0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x220): multiple definition of `__signbit'
DeclareAll.o:DeclareAll.c:(.text+0x220): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x240): multiple definition of `__signbitf'
DeclareAll.o:DeclareAll.c:(.text+0x240): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x260): multiple definition of `__signbitl'
DeclareAll.o:DeclareAll.c:(.text+0x260): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x280): multiple definition of `sinhf'
DeclareAll.o:DeclareAll.c:(.text+0x280): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x2a0): multiple definition of `coshf'
DeclareAll.o:DeclareAll.c:(.text+0x2a0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x2c0): multiple definition of `tanhf'
DeclareAll.o:DeclareAll.c:(.text+0x2c0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x2e0): multiple definition of `expf'
DeclareAll.o:DeclareAll.c:(.text+0x2e0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x300): multiple definition of `frexpf'
DeclareAll.o:DeclareAll.c:(.text+0x300): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x320): multiple definition of `ldexpf'
DeclareAll.o:DeclareAll.c:(.text+0x320): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x340): multiple definition of `logb'
DeclareAll.o:DeclareAll.c:(.text+0x340): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x370): multiple definition of `logbf'
DeclareAll.o:DeclareAll.c:(.text+0x370): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x3a0): multiple definition of `logbl'
DeclareAll.o:DeclareAll.c:(.text+0x3a0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x3d0): multiple definition of `fabsf'
DeclareAll.o:DeclareAll.c:(.text+0x3d0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x3f0): multiple definition of `fabsl'
DeclareAll.o:DeclareAll.c:(.text+0x3f0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x420): multiple definition of `hypotf'
DeclareAll.o:DeclareAll.c:(.text+0x420): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x450): multiple definition of `powf'
DeclareAll.o:DeclareAll.c:(.text+0x450): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x480): multiple definition of `rint'
DeclareAll.o:DeclareAll.c:(.text+0x480): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x4a0): multiple definition of `rintf'
DeclareAll.o:DeclareAll.c:(.text+0x4a0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x4c0): multiple definition of `rintl'
DeclareAll.o:DeclareAll.c:(.text+0x4c0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x4f0): multiple definition of `lrint'
DeclareAll.o:DeclareAll.c:(.text+0x4f0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x510): multiple definition of `lrintf'
DeclareAll.o:DeclareAll.c:(.text+0x510): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x530): multiple definition of `lrintl'
DeclareAll.o:DeclareAll.c:(.text+0x530): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x550): multiple definition of `llrint'
DeclareAll.o:DeclareAll.c:(.text+0x550): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x570): multiple definition of `llrintf'
DeclareAll.o:DeclareAll.c:(.text+0x570): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x590): multiple definition of `llrintl'
DeclareAll.o:DeclareAll.c:(.text+0x590): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x5b0): multiple definition of `strncasecmp'
DeclareAll.o:DeclareAll.c:(.text+0x5b0): first defined here
NormalizeProbes.o:NormalizeProbes.c:(.text+0x5d0): multiple definition of `strcasecmp'
DeclareAll.o:DeclareAll.c:(.text+0x5d0): first defined here
collect2: ld returned 1 exit status
ERROR: compilation failed for package 'rMAT'
* removing 'D:/biocbld/bbs-2.8-bioc/tmpdir/Rtmp2SFxUj/Rinst68472d54/rMAT'
-----------------------------------
ERROR: package installation failed