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BioC 3.5: CHECK report for VariantFiltering on oaxaca

This page was generated on 2017-01-16 16:36:24 -0500 (Mon, 16 Jan 2017).

Package 1299/1323HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.11.2
Robert Castelo
Snapshot Date: 2017-01-15 17:16:07 -0500 (Sun, 15 Jan 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VariantFiltering
Last Changed Rev: 125469 / Revision: 125950
Last Changed Date: 2016-12-28 12:43:39 -0500 (Wed, 28 Dec 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: VariantFiltering
Version: 1.11.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VariantFiltering_1.11.2.tar.gz
StartedAt: 2017-01-16 08:36:48 -0800 (Mon, 16 Jan 2017)
EndedAt: 2017-01-16 08:43:59 -0800 (Mon, 16 Jan 2017)
EllapsedTime: 430.4 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_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/VariantFiltering.Rcheck’
* using R Under development (unstable) (2016-10-26 r71594)
* 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 ‘1.11.2’
* 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 ... 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 objects imported by ':::' calls:
  'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs'
  'VariantAnnotation:::.consolidateHits'
  'VariantAnnotation:::.returnEmpty'
  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:
  '.adjustForStrandSense'
* 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 ... NOTE
Package unavailable to check Rd xrefs: ‘phastCons100way.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 ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
VariantFilteringParam-class 3.25   0.32  14.242
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c:99:7: warning: unused variable 'nsco' [-Wunused-variable]
  int nsco = INTEGER(nscoR)[0];
      ^
methods-WeightMatrix.c:100:11: warning: unused variable 'scores' [-Wunused-variable]
  double* scores;
          ^
methods-WeightMatrix.c:129:7: warning: unused variable 'nsco' [-Wunused-variable]
  int nsco = INTEGER(nscoR)[0];
      ^
methods-WeightMatrix.c:131:11: warning: unused variable 'scores' [-Wunused-variable]
  double* scores;
          ^
4 warnings 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-3.5-bioc/meat/VariantFiltering.Rcheck/VariantFiltering/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantFiltering)

VariantFiltering.Rcheck/VariantFiltering-Ex.timings:

nameusersystemelapsed
GenePhylostrataDb-class0.0010.0000.001
MafDb-class0.0010.0000.001
MafDb2-class1.1940.0301.572
PhastConsDb-class2.2740.1252.601
VariantFilteringParam-class 3.250 0.32014.242
VariantFilteringResults-class0.0020.0000.003
VariantType-class0.0020.0010.002
WeightMatrix-class0.0080.0010.010
autosomalDominant0.0000.0000.001
autosomalRecessiveHeterozygous0.0000.0000.001
autosomalRecessiveHomozygous0.0010.0000.000
deNovo000
readAAradicalChangeMatrix0.0060.0010.007
unrelatedIndividuals0.0000.0000.001
xLinked0.0010.0000.001