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Package 288/354HostnameOS / ArchBUILDCHECKBUILD BIN
rMAT 2.3.3
Arnaud Droit and Raphael Gottardo
Bioconductor Changelog
Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rMAT
Last Changed Rev: 43398 / Revision: 43434
Last Changed Date: 2009-12-04 14:24:17 -0800 (Fri, 04 Dec 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: rMAT
Version: 2.3.3
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes rMAT_2.3.3.tar.gz
StartedAt: 2009-12-07 18:17:49 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 18:19:25 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 96.2 seconds
RetCode: 0
Status: OK
CheckDir: rMAT.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/rMAT.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rMAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rMAT' version '2.3.3'
* 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 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 name space can be loaded with stated dependencies ... 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 ... OK
* checking Rd \usage sections ... 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

rMAT.Rcheck/00install.out:

* install options are ' --no-html'

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

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


** libs
  making DLL ...
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O2 -Wall  -c BARFileData.cpp -o BARFileData.o
In file included from BARFileData.cpp:20:
BARFileData.h:29: warning: ignoring #pragma warning 
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O2 -Wall  -c BARFileWriter.cpp -o BARFileWriter.o
In file included from BARFileWriter.cpp:20:
BARFileWriter.h:29: warning: ignoring #pragma warning 
In file included from BARFileWriter.h:34,
                 from BARFileWriter.cpp:20:
BARFileData.h:29: warning: ignoring #pragma warning 
BARFileWriter.cpp:33: warning: ignoring #pragma warning 
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O2 -Wall  -c BARReader.cpp -o BARReader.o
In file included from BARReader.cpp:28:
BARFileData.h:29: warning: ignoring #pragma warning 
In file included from e:/biocbld/bbs-2.6-bioc/R/include/R.h:50,
                 from BARReader.cpp:39:
e:/biocbld/bbs-2.6-bioc/R/include/R_ext/RS.h:43:1: warning: "ERROR" redefined
In file included from c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/windows.h:52,
                 from BARFileData.h:30,
                 from BARReader.cpp:28:
c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/wingdi.h:313:1: warning: this is the location of the previous definition
BARReader.cpp: In function 'SEXPREC* Parser(SEXPREC*)':
BARReader.cpp:258: warning: unused variable 'buf'
BARReader.cpp: In function 'SEXPREC* ParseMATBar(SEXPREC*)':
BARReader.cpp:472: warning: unused variable 'regionR'
BARReader.cpp:473: warning: unused variable 'p_region'
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O2 -Wall  -c BARWriter.cpp -o BARWriter.o
In file included from BARWriter.cpp:30:
BARFileWriter.h:29: warning: ignoring #pragma warning 
In file included from BARFileWriter.h:34,
                 from BARWriter.cpp:30:
BARFileData.h:29: warning: ignoring #pragma warning 
In file included from e:/biocbld/bbs-2.6-bioc/R/include/R.h:50,
                 from BARWriter.cpp:40:
e:/biocbld/bbs-2.6-bioc/R/include/R_ext/RS.h:43:1: warning: "ERROR" redefined
In file included from c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/windows.h:52,
                 from BARFileData.h:30,
                 from BARFileWriter.h:34,
                 from BARWriter.cpp:30:
c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/wingdi.h:313:1: warning: this is the location of the previous definition
BARWriter.cpp: In function 'SEXPREC* WriteBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
BARWriter.cpp:87: warning: unused variable 'signal2Length'
BARWriter.cpp:90: warning: unused variable 'lengthList'
BARWriter.cpp:91: warning: unused variable 'curListPtr'
BARWriter.cpp:91: warning: unused variable 'startListPtr'
BARWriter.cpp:92: warning: unused variable 'curChromosome'
BARWriter.cpp:93: warning: unused variable 'i'
BARWriter.cpp: In function 'SEXPREC* WriteNormalizedBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
BARWriter.cpp:271: warning: unused variable 'addPos'
BARWriter.cpp: In function 'SEXPREC* testBAR(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
BARWriter.cpp:78: warning: control reaches end of non-void function
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O2 -Wall  -c BPMAPFileData.cpp -o BPMAPFileData.o
In file included from BPMAPFileData.cpp:21:
BPMAPFileData.h:30: warning: ignoring #pragma warning 
BPMAPFileData.cpp: In member function 'bool affxbpmap::CBPMAPFileData::ReadDataSection()':
BPMAPFileData.cpp:374: warning: unused variable 'probeIn'
BPMAPFileData.cpp:375: warning: unused variable 'probeOut'
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O2 -Wall  -c BPMAPfunctions.cpp -o BPMAPfunctions.o
In file included from BPMAPfunctions.cpp:9:
BPMAPFileData.h:30: warning: ignoring #pragma warning 
In file included from e:/biocbld/bbs-2.6-bioc/R/include/R.h:50,
                 from BPMAPfunctions.cpp:17:
e:/biocbld/bbs-2.6-bioc/R/include/R_ext/RS.h:43:1: warning: "ERROR" redefined
In file included from c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/windows.h:52,
                 from BPMAPFileData.h:31,
                 from BPMAPfunctions.cpp:9:
c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/wingdi.h:313:1: warning: this is the location of the previous definition
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O3 -Wall  -std=gnu99 -c DeclareAll.c -o DeclareAll.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O2 -Wall  -c FileIO.cpp -o FileIO.o
FileIO.cpp:32: warning: ignoring #pragma warning 
FileIO.cpp: In function 'float MmGetFloat_I(float*)':
FileIO.cpp:362: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function 'void MmSetFloat_I(float*, float)':
FileIO.cpp:367: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function 'float MmGetFloat_N(float*)':
FileIO.cpp:373: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileIO.cpp: In function 'void MmSetFloat_N(float*, float)':
FileIO.cpp:378: warning: dereferencing type-punned pointer will break strict-aliasing rules
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/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: warning: dereferencing type-punned pointer will break strict-aliasing rules
FileWriter.cpp: In function 'void WriteFloat_N(std::ofstream&, float)':
FileWriter.cpp:113: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -Ie:/biocbld/bbs-2.6-bioc/R/src/include -IC:/gsl/include       -O3 -Wall  -std=gnu99 -c NormalizeProbes.c -o NormalizeProbes.o
NormalizeProbes.c: In function 'normArray':
NormalizeProbes.c:1052: warning: suggest parentheses around comparison in operand of &
g++ -shared -s -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-2.6-bioc/R/bin -lR
  ... done
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 Map,
	 cbind,
	 mapply,
	 order,
	 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 ...
** MD5 sums
* DONE (rMAT)