crlmm 1.2.4
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/crlmm | | Last Changed Rev: 40625 / Revision: 42512 | | Last Changed Date: 2009-07-14 17:21:23 -0700 (Tue, 14 Jul 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 |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/crlmm.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'crlmm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'crlmm' version '1.2.4'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'crlmm' 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 files against version 2 parser ... 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 use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'crlmm' ...
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c gtypeCaller.c -o gtypeCaller.o
gtypeCaller.c: In function 'gtypeCallerPart1':
gtypeCaller.c:87: warning: unused variable 'ibv2'
gtypeCaller.c: In function 'gtypeCallerPart2':
gtypeCaller.c:310: warning: unused variable 'ibv2'
gtypeCaller.c:310: warning: unused variable 'ibv1'
gtypeCaller.c:307: warning: unused variable 'lenLists'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c gtypeCallerNM.c -o gtypeCallerNM.o
gtypeCallerNM.c: In function 'gtypeCallerPart1nm':
gtypeCallerNM.c:212: warning: implicit declaration of function 'mad_median'
gtypeCallerNM.c:87: warning: unused variable 'ibv2'
gtypeCallerNM.c: In function 'gtypeCallerPart2nm':
gtypeCallerNM.c:310: warning: unused variable 'ibv2'
gtypeCallerNM.c:310: warning: unused variable 'ibv1'
gtypeCallerNM.c:307: warning: unused variable 'lenLists'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c gtypeCallerNormalNoN.c -o gtypeCallerNormalNoN.o
gtypeCallerNormalNoN.c: In function 'gtypeCallerPart1NormalNoN':
gtypeCallerNormalNoN.c:87: warning: unused variable 'ibv2'
gtypeCallerNormalNoN.c: In function 'gtypeCallerPart2NormalNoN':
gtypeCallerNormalNoN.c:292: warning: unused variable 'ibv2'
gtypeCallerNormalNoN.c:292: warning: unused variable 'ibv1'
gtypeCallerNormalNoN.c:289: warning: unused variable 'lenLists'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c gtypeCallerTNoN.c -o gtypeCallerTNoN.o
gtypeCallerTNoN.c: In function 'gtypeCallerPart1TNoN':
gtypeCallerTNoN.c:87: warning: unused variable 'ibv2'
gtypeCallerTNoN.c: In function 'gtypeCallerPart2TNoN':
gtypeCallerTNoN.c:292: warning: unused variable 'ibv2'
gtypeCallerTNoN.c:292: warning: unused variable 'ibv1'
gtypeCallerTNoN.c:289: warning: unused variable 'lenLists'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c init.c -o init.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c tmp.c -o tmp.o
tmp.c: In function 'test':
tmp.c:17: warning: implicit declaration of function 'genotypeConfidence'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c trimmed.c -o trimmed.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124: warning: unused variable 'n_ignore'
gcc -shared -s -o crlmm.dll tmp.def gtypeCaller.o gtypeCallerNM.o gtypeCallerNormalNoN.o gtypeCallerTNoN.o init.o tmp.o trimmed.o utils.o -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
*** installing help indices
>>> Building/Updating help pages for package 'crlmm'
Formats: text html latex example chm
celDates text html latex chm
cnrma text html latex example chm
computeCopynumber text html latex chm
crlmm-package text html latex chm
crlmm text html latex example chm
crlmmIllumina text html latex example chm
list.celfiles text html latex example chm
methods-SnpSet text html latex example chm
readIdatFiles text html latex example chm
snprma text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\CRLMM~1.RCH\00_PKG~1\crlmm\chm\crlmm.chm
Compile time: 0 minutes, 0 seconds
11 Topics
23 Local links
0 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\CRLMM~1.RCH\00_PKG~1\crlmm\chm\crlmm.chm, 33,722 bytes
Compression decreased file by 13,857 bytes.
** building package indices ...
** MD5 sums
* DONE (crlmm)