crlmm 1.11.2
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm | | Last Changed Rev: 55182 / Revision: 55359 | | Last Changed Date: 2011-04-30 04:38:33 -0700 (Sat, 30 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 | OK | [ WARNINGS ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/crlmm.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-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 '1.11.2'
* 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 installed package size ... NOTE
installed size is 12.8Mb
sub-directories of 1Mb or more:
doc 10.8Mb
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 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 ... NOTE
computeSummary: no visible global function definition for
'summaryStats'
genotypeInf: no visible binding for global variable 'cdfName'
linesCNSet: no visible global function definition for 'llines'
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 ... 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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
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 ... OK
* 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 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' ... WARNING
Package vignette(s) without corresponding PDF:
'CopyNumberOverview.Rnw'
'genotyping.Rnw'
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'D:/biocbld/bbs-2.9-bioc/meat/crlmm.Rcheck/00check.log'
for details
* installing *source* package 'crlmm' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -c gtypeCaller.c -o gtypeCaller.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -c init.c -o init.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -c trimmed.c -o trimmed.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124:15: warning: unused variable 'n_ignore'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/crlmm.Rcheck/crlmm/libs/x64
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Loading package bit1.1-7
package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Loading package ff2.2-2
- getOption("fftempdir")=="D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpWMYT9p"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==42928701.44 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==2146435072 -- consider a different value for tuning your system
Creating a new generic function for "lines" in "crlmm"
** 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
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Welcome to crlmm version 1.11.2
* DONE (crlmm)