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Package 121/514HostnameOS / ArchBUILDCHECKBUILD BIN
crlmm 1.12.1
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/crlmm
Last Changed Rev: 61976 / Revision: 64395
Last Changed Date: 2012-01-10 19:39:25 -0800 (Tue, 10 Jan 2012)
wilson2 Linux (openSUSE 11.4) / x86_64  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  OK 

Summary

Package: crlmm
Version: 1.12.1
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings crlmm_1.12.1.tar.gz
StartedAt: 2012-03-23 23:59:44 -0700 (Fri, 23 Mar 2012)
EndedAt: 2012-03-24 00:06:39 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 414.6 seconds
RetCode: 0
Status:  OK 
CheckDir: crlmm.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/crlmm.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 22.7Mb
  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 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 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’
getBAF: no visible binding for global variable ‘ct’
getTau2: no visible binding for global variable ‘nmb’
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

crlmm.Rcheck/00install.out:

* installing *source* package ‘crlmm’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c gtypeCaller.c -o gtypeCaller.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c trimmed.c -o trimmed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/crlmm.Rcheck/crlmm/libs
** 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)

crlmm.Rcheck/crlmm-Ex.timings:

nameusersystemelapsed
PredictionRegion-class0.0000.0000.002
batchStatisticAccessors3.5480.0283.576
calculateRBaf2.5360.0202.555
cnSetExample1.0680.0081.107
constructInf0.0000.0000.001
copynumberAccessors1.0600.0081.099
crlmm137.349 2.456144.685
crlmmIllumina000
crlmmIlluminaV2000
genotype.Illumina000
genotype0.1040.0080.112
genotypeInf0.0000.0000.001
genotypes0.0040.0000.001
posteriorProbability6.0400.0606.369
predictionRegion1.1200.0041.205
preprocessInf0.0000.0000.001
readGenCallOutput000
readIDAT000
readIdatFiles0.0000.0000.001
snprma26.510 1.43628.726
xyplot0.5280.0040.536