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BioC 3.0: CHECK report for crlmm on zin1

This page was generated on 2015-04-10 09:38:27 -0700 (Fri, 10 Apr 2015).

Package 210/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crlmm 1.24.0
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/crlmm
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: crlmm
Version: 1.24.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings crlmm_1.24.0.tar.gz
StartedAt: 2015-04-09 23:00:01 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:12:08 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 727.6 seconds
RetCode: 0
Status:  OK 
CheckDir: crlmm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings crlmm_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/crlmm.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.24.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘crlmm’ can be installed ... [22s/22s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘preprocessCore’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘SNPchip’ ‘ff’ ‘splines’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
calculateRBafCNSet : processByChromosome: no visible global function
  definition for ‘position’
cnrmaAffy: no visible global function definition for ‘celfileName’
computeBR: no visible global function definition for ‘genomeBuild’
constructBafLrrSetListFrom: no visible global function definition for
  ‘genomeBuild’
constructOligoSetListFrom: no visible global function definition for
  ‘genomeBuild’
snprmaAffy: no visible global function definition for ‘celfileName’
* 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 ... OK
* 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 GNU extensions in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [257s/260s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
crlmm    109.843  1.208 111.941
genotype 105.491  1.572 108.583
snprma    19.309  0.676  20.017
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘crlmm_unit_tests.R’ [123s/123s]
  Running ‘doRUnit.R’ [126s/127s]
 [249s/250s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/crlmm.Rcheck/00check.log’
for details.

crlmm.Rcheck/00install.out:

* installing *source* package ‘crlmm’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c gtypeCaller.c -o gtypeCaller.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/crlmm.Rcheck/crlmm/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (crlmm)

crlmm.Rcheck/crlmm-Ex.timings:

nameusersystemelapsed
ListClassConstructors2.2120.0282.263
PredictionRegion-class0.0000.0000.002
batchStatisticAccessors0.5480.0080.561
calculateRBaf0.6480.0120.670
celfile-utils1.5520.2042.005
cnSetExample0.7800.0160.801
constructInf000
copynumberAccessors0.0000.0000.001
crlmm109.843 1.208111.941
crlmmIllumina000
crlmmIlluminaV2000
genotype.Illumina0.0000.0000.002
genotype105.491 1.572108.583
genotypeInf0.0000.0000.001
genotypes0.0040.0000.004
posteriorProbability1.6400.0281.684
predictionRegion0.3600.0120.370
preprocessInf0.0000.0000.001
readGenCallOutput0.0000.0000.001
readIdatFiles000
snprma19.309 0.67620.017
validCdfNames0.0000.0000.001
xyplot1.1760.0161.196