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BioC 3.0: CHECK report for crlmm on oaxaca

This page was generated on 2015-04-10 10:03:30 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch crlmm_1.24.0.tar.gz
StartedAt: 2015-04-09 22:41:17 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:55:57 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 880.4 seconds
RetCode: 0
Status:  OK 
CheckDir: crlmm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch crlmm_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/crlmm.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [25s/26s] OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [300s/312s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
crlmm    126.658  2.492 129.653
genotype 118.557  5.525 135.001
snprma    21.145  0.944  22.493
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘crlmm_unit_tests.R’ [145s/146s]
  Running ‘doRUnit.R’ [148s/149s]
 [293s/295s] 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/crlmm.Rcheck/00check.log’
for details.

crlmm.Rcheck/00install.out:

* installing *source* package ‘crlmm’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gtypeCaller.c -o gtypeCaller.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c trimmed.c -o trimmed.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c utils.c -o utils.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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
ListClassConstructors2.3950.0432.443
PredictionRegion-class0.0020.0010.002
batchStatisticAccessors0.6350.0210.664
calculateRBaf0.7460.0270.780
celfile-utils3.6780.2984.217
cnSetExample0.8790.0820.964
constructInf0.0000.0000.001
copynumberAccessors0.0010.0000.002
crlmm126.658 2.492129.653
crlmmIllumina0.0010.0010.000
crlmmIlluminaV20.0010.0000.000
genotype.Illumina0.0020.0000.002
genotype118.557 5.525135.001
genotypeInf0.0000.0000.001
genotypes0.0030.0000.004
posteriorProbability1.7030.1821.885
predictionRegion1.0830.0941.179
preprocessInf0.0000.0000.001
readGenCallOutput000
readIdatFiles0.0010.0000.000
snprma21.145 0.94422.493
validCdfNames0.0010.0010.002
xyplot0.6400.0390.680