rMAT 3.3.0
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rMAT | | Last Changed Rev: 56153 / Revision: 56603 | | Last Changed Date: 2011-06-13 15:40:41 -0700 (Mon, 13 Jun 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | N O T S U P P O R T E D |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/rMAT.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rMAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rMAT' version '3.3.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rMAT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions/methods with usage in documentation object 'tilingSet' but not in code:
new
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'NormalizeProbes'
'standard'
Objects in \usage without \alias in documentation object 'tilingSet':
'new'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings, see
'E:/biocbld/bbs-2.9-bioc/meat/rMAT.Rcheck/00check.log'
for details
* installing *source* package 'rMAT' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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˜1.9-B/R/include/R.h:44:0,
from BARReader.cpp:39:
E:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools213\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˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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˜1.9-B/R/include/R.h:44:0,
from BARWriter.cpp:40:
E:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools213\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˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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˜1.9-B/R/include/R.h:44:0,
from BPMAPfunctions.cpp:17:
E:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools213\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˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/include -O3 -Wall -std=gnu99 -c DeclareAll.c -o DeclareAll.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/GSL/i386/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/i386/lib -lgsl -lgslcblas -lm -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/rMAT.Rcheck/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, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. 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 ...
*** tangling vignette sources ...
'rMAT.Rnw'
** testing if installed package can be loaded
* DONE (rMAT)