BioC 2.13: CHECK report for crlmm on perceval

Package: crlmm

Version: 1.20.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch crlmm_1.20.4.tar.gz

StartedAt: 2014-04-05 00:36:25 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:02:12 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 1547.5 seconds

RetCode: 0

Status:  OK

CheckDir: crlmm.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/crlmm.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.20.4’
* 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 ... [36s/45s] 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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ellipse’ ‘VGAM’
A package should be listed in only one of these fields.
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
Namespaces in Imports field not imported from:
  ‘ff’ ‘SNPchip’ ‘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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘calculateRTheta’ ‘processIDAT’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [7m/13m] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
genotype      174.967 32.036 542.420
crlmm         151.596  5.726 158.086
snprma         25.597  2.805  28.533
celfile-utils   2.684  0.506   5.252
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘crlmm_unit_tests.R’ [193s/196s]
  Running ‘doRUnit.R’ [195s/198s]
 [389s/394s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/crlmm.Rcheck/00check.log’
for details.

* installing *source* package ‘crlmm’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c gtypeCaller.c -o gtypeCaller.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c trimmed.c -o trimmed.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c utils.c -o utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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-2.13-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)

name	user	system	elapsed
ListClassConstructors	4.302	0.087	4.391
PredictionRegion-class	0.011	0.004	0.015
batchStatisticAccessors	0.838	0.034	0.872
calculateRBaf	0.964	0.038	1.002
celfile-utils	2.684	0.506	5.252
cnSetExample	1.114	0.158	1.273
constructInf	0.003	0.006	0.008
copynumberAccessors	0.006	0.011	0.015
crlmm	151.596	5.726	158.086
crlmmIllumina	0.002	0.004	0.005
crlmmIlluminaV2	0.002	0.005	0.007
genotype.Illumina	0.006	0.020	0.027
genotype	174.967	32.036	542.420
genotypeInf	0.002	0.004	0.006
genotypes	0.007	0.005	0.013
posteriorProbability	2.567	0.617	3.254
predictionRegion	0.941	0.177	1.150
preprocessInf	0.002	0.004	0.005
readGenCallOutput	0.002	0.003	0.005
readIdatFiles	0.002	0.004	0.006
snprma	25.597	2.805	28.533
validCdfNames	0.002	0.004	0.006
xyplot	0.734	0.118	0.853