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BioC 2.14: CHECK report for VariantFiltering on morelia

This page was generated on 2014-10-08 09:07:50 -0700 (Wed, 08 Oct 2014).

Package 804/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.0.4
Robert Castelo
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/VariantFiltering
Last Changed Rev: 91489 / Revision: 95116
Last Changed Date: 2014-06-16 14:56:15 -0700 (Mon, 16 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: VariantFiltering
Version: 1.0.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch VariantFiltering_1.0.4.tar.gz
StartedAt: 2014-10-08 02:05:04 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:09:38 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 273.4 seconds
RetCode: 0
Status:  OK 
CheckDir: VariantFiltering.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch VariantFiltering_1.0.4.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/VariantFiltering.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantFiltering/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantFiltering’ version ‘1.0.4’
* 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 ‘VariantFiltering’ can be installed ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 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 ... [28s/32s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
PhastConsDb-class           11.466  0.597  12.070
VariantFilteringParam-class  2.193  0.134   6.369
* 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

VariantFiltering.Rcheck/00install.out:

* installing *source* package ‘VariantFiltering’ ...
** 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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_VariantFiltering.c -o R_init_VariantFiltering.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c:122:23: warning: unused variable 'k' [-Wunused-variable]
  int S_length, i, j, k;
                      ^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/VariantFiltering.Rcheck/VariantFiltering/libs
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (VariantFiltering)

VariantFiltering.Rcheck/VariantFiltering-Ex.timings:

nameusersystemelapsed
GenePhylostrataDb-class0.0010.0000.001
MafDb-class1.7530.3242.355
PhastConsDb-class11.466 0.59712.070
VariantFilteringParam-class2.1930.1346.369
VariantFilteringResults-class0.0020.0000.003
WeightMatrix-class0.0120.0020.014
allInheritanceModels0.0000.0000.001
autosomalDominant0.0010.0000.000
autosomalRecessiveHeterozygous0.0010.0000.001
autosomalRecessiveHomozygous0.0000.0000.001
deNovo0.0010.0000.000
readAAradicalChangeMatrix0.0080.0010.010
unrelatedIndividuals0.0000.0000.001
xLinked0.0010.0000.001