crlmm 1.12.1
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/crlmm | | Last Changed Rev: 60337 / Revision: 61898 | | Last Changed Date: 2011-11-15 11:00:53 -0800 (Tue, 15 Nov 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | ERROR |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/crlmm.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'crlmm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'crlmm' version '1.12.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'crlmm' can be installed ... OK
* checking installed package size ... NOTE
installed size is 22.6Mb
sub-directories of 1Mb or more:
data 9.5Mb
doc 11.0Mb
scripts 1.6Mb
* 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... NOTE
.bivariateCenter: no visible binding for global variable 'Sigma'
computeSummary: no visible global function definition for
'summaryStats'
genotypeInf: no visible binding for global variable 'cdfName'
getBAF: no visible binding for global variable 'ct'
getTau2: no visible binding for global variable 'nmb'
preprocess: no visible binding for global variable 'cdfName'
preprocessInf: no visible binding for global variable 'cdfName'
updateCors: no visible binding for global variable 'index'
updateStats: no visible global function definition for 'Ns.AA'
updateStats: no visible global function definition for 'Ns.AA<-'
updateStats: no visible binding for global variable 'k'
updateStats: no visible binding for global variable 'G.call'
updateStats: no visible global function definition for 'Ns.AB'
updateStats: no visible global function definition for 'Ns.AB<-'
updateStats: no visible global function definition for 'Ns.BB'
updateStats: no visible global function definition for 'Ns.BB<-'
updateTau: no visible global function definition for 'summaryStats'
* checking Rd files ... NOTE
prepare_Rd: ABpanel.Rd:38-40: Dropping empty section \details
* 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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
* checking data for ASCII and uncompressed saves ... NOTE
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
cnSetExample.rda 8.1Mb 6.0Mb xz
cnSetExample2.rda 1.5Mb 1.1Mb xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'crlmm_unit_tests.R'
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
* installing *source* package 'crlmm' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c gtypeCaller.c -o gtypeCaller.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124:15: warning: unused variable 'n_ignore'
utils.c: In function 'normalizeBAF':
utils.c:178:7: warning: suggest parentheses around comparison in operand of '&'
utils.c:180:7: warning: suggest parentheses around comparison in operand of '&'
gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/crlmm.Rcheck/crlmm/libs/i386
** R
** data
** inst
** preparing package for lazy loading
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'AffymetrixPreprocessCN.Rnw'
'CopyNumberOverview.Rnw'
'IlluminaPreprocessCN.Rnw'
'Infrastructure.Rnw'
'copynumber.Rnw'
'crlmmDownstream.Rnw'
'genotyping.Rnw'
** testing if installed package can be loaded
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
* DONE (crlmm)