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BioC 3.1: CHECK report for VariantFiltering on morelia

This page was generated on 2015-10-09 09:41:46 -0700 (Fri, 09 Oct 2015).

Package 1004/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.4.3
Robert Castelo
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/VariantFiltering
Last Changed Rev: 104183 / Revision: 109384
Last Changed Date: 2015-05-25 08:26:20 -0700 (Mon, 25 May 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantFiltering
Version: 1.4.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VariantFiltering_1.4.3.tar.gz
StartedAt: 2015-10-09 07:07:55 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 07:11:42 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 226.6 seconds
RetCode: 0
Status:  OK 
CheckDir: VariantFiltering.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VariantFiltering_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/VariantFiltering.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.3’
* 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 ... [25s/25s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::labeledLine’
  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
allVariants,VariantFilteringResults : .local: no visible global
  function definition for ‘sampleNames’
autosomalDominant,VariantFilteringParam : .local: no visible global
  function definition for ‘extractSeqlevelsByGroup’
autosomalRecessiveHeterozygous,VariantFilteringParam : .local: no
  visible global function definition for ‘extractSeqlevelsByGroup’
autosomalRecessiveHomozygous,VariantFilteringParam : .local: no visible
  global function definition for ‘extractSeqlevelsByGroup’
filteredVariants,VariantFilteringResults : .local: no visible global
  function definition for ‘softFilter’
filteredVariants,VariantFilteringResults : .local: no visible global
  function definition for ‘sampleNames<-’
filteredVariants,VariantFilteringResults : .local: no visible global
  function definition for ‘sampleNames’
plot,VariantFilteringResults-ANY : .local: no visible global function
  definition for ‘sprintF’
plot,VariantFilteringResults-ANY : .local: no visible global function
  definition for ‘restoreSeqlevels’
reportVariants,VariantFilteringResults : .local : <anonymous>: no
  visible binding for global variable ‘totalDepth’
scores,PhastConsDb-GRanges : .local: no visible global function
  definition for ‘seqleveslStyle<-’
xLinked,VariantFilteringParam : .local: no visible global function
  definition for ‘extractSeqlevelsByGroup’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘phastCons7way.UCSC.hg38’
* 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 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 ... [14s/24s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
VariantFilteringParam-class 2.703  0.357  11.606
* 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

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/VariantFiltering.Rcheck/00check.log’
for details.


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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c:123:23: 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/Library/Frameworks/R.framework/Resources/lib -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-3.1-bioc/meat/VariantFiltering.Rcheck/VariantFiltering/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (VariantFiltering)

VariantFiltering.Rcheck/VariantFiltering-Ex.timings:

nameusersystemelapsed
GenePhylostrataDb-class0.0010.0000.001
MafDb-class0.1120.0220.333
PhastConsDb-class1.3070.0462.328
VariantFilteringParam-class 2.703 0.35711.606
VariantFilteringResults-class0.0020.0000.002
WeightMatrix-class0.0060.0000.007
autosomalDominant0.0010.0000.001
autosomalRecessiveHeterozygous0.0000.0010.001
autosomalRecessiveHomozygous0.0010.0000.001
deNovo0.0010.0000.000
readAAradicalChangeMatrix0.0070.0000.007
unrelatedIndividuals0.0010.0000.001
xLinked0.0010.0000.001