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Package 73/319HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: crlmm
Version: 1.2.4
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD check --no-vignettes crlmm_1.2.4.tar.gz
StartedAt: 2009-10-20 15:58:11 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 16:00:54 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 162.7 seconds
RetCode: 0
Status: OK
CheckDir: crlmm.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/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 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 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

crlmm.Rcheck/00install.out:

* Installing *source* package 'crlmm' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c tmp.c -o tmp.o
tmp.c: In function 'test':
tmp.c:17: warning: implicit declaration of function 'genotypeConfidence'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124: warning: unused variable 'n_ignore'
gcc -std=gnu99 -shared -L/usr/local/lib64 -o crlmm.so gtypeCaller.o gtypeCallerNM.o gtypeCallerNormalNoN.o gtypeCallerTNoN.o init.o tmp.o trimmed.o utils.o -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
 >>> Building/Updating help pages for package 'crlmm'
     Formats: text html latex example 
  celDates                          text    html    latex
  cnrma                             text    html    latex   example
  computeCopynumber                 text    html    latex
  crlmm-package                     text    html    latex
  crlmm                             text    html    latex   example
  crlmmIllumina                     text    html    latex   example
  list.celfiles                     text    html    latex   example
  methods-SnpSet                    text    html    latex   example
  readIdatFiles                     text    html    latex   example
  snprma                            text    html    latex   example
** building package indices ...
* DONE (crlmm)