rMAT 3.3.0
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rMAT | | Last Changed Rev: 54811 / Revision: 55359 | | Last Changed Date: 2011-04-13 18:45:05 -0700 (Wed, 13 Apr 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 |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/rMAT.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
‘/loc/home/biocbuild/bbs-2.9-bioc/meat/rMAT.Rcheck/00check.log’
for details
* installing *source* package ‘rMAT’ ...
R_HOME: /home/biocbuild/bbs-2.9-bioc/R
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... no
checking dispatch/dispatch.h presence... no
checking for dispatch/dispatch.h... no
checking omp.h usability... yes
checking omp.h presence... yes
checking for omp.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BARFileData.cpp -o BARFileData.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BARFileWriter.cpp -o BARFileWriter.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BARReader.cpp -o BARReader.o
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/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BARWriter.cpp -o BARWriter.o
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/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BPMAPFileData.cpp -o BPMAPFileData.o
BPMAPFileData.cpp: In member function ‘bool affxbpmap::CBPMAPFileData::ReadDataSection()’:
BPMAPFileData.cpp:379:7: warning: unused variable ‘hitSize’
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BPMAPfunctions.cpp -o BPMAPfunctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DeclareAll.c -o DeclareAll.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c FileIO.cpp -o FileIO.o
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:378:19: warning: dereferencing type-punned pointer will break strict-aliasing rules
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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 -L/usr/local/lib64 -o rMAT.so BARFileData.o BARFileWriter.o BARReader.o BARWriter.o BPMAPFileData.o BPMAPfunctions.o DeclareAll.o FileIO.o FileWriter.o NormalizeProbes.o -lgsl -lgslcblas -lm -lgomp -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/rMAT.Rcheck/rMAT/libs
** 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)