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BioC 2.12: CHECK report for GeneticsPed on petty

This page was generated on 2013-10-09 09:39:35 -0700 (Wed, 09 Oct 2013).

Package 265/671HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.22.0
David Henderson
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GeneticsPed
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GeneticsPed
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneticsPed_1.22.0.tar.gz
StartedAt: 2013-10-08 22:31:50 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:32:53 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 62.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneticsPed.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.22.0'
* 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 'GeneticsPed' can be installed ... [14s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 for unstated 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 ... NOTE
gpLong2Wide: warning in expectedGenotypes(allele = allele.names(x[,
  genotype])): partial argument match of 'allele' to 'alleles'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.Pedigree':
  'summary.Pedigree'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [2s/2s]
 [3s/3s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GeneticsPed.Rcheck/00check.log'
for details.

GeneticsPed.Rcheck/00install.out:

* installing *source* package 'GeneticsPed' ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c ainverse.cc -o ainverse.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c eibd.cc -o eibd.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c ggmatmult.f -o ggmatmult.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c gpi.f -o gpi.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c inbreed.cc -o inbreed.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c inverseAdditive.cc -o inverseAdditive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c meuwissen.cc -o meuwissen.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c pedSort.cc -o pedSort.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c pedtemplate.cc -o pedtemplate.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c register.cc -o register.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c sargolzaei.c -o sargolzaei.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c sortped.cc -o sortped.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o GeneticsPed.so ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/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 (GeneticsPed)

GeneticsPed.Rcheck/GeneticsPed-Ex.timings:

nameusersystemelapsed
TDT0.0920.0050.097
check0.1810.0060.190
datasets0.0460.0030.051
extend0.2180.0100.229
family0.0800.0030.083
founder0.0190.0010.020
geneContribution0.1310.0110.142
generatePedigree0.0860.0490.137
generation0.1160.0020.118
gpi0.0650.0030.069
gpiUtil0.0270.0000.027
inbreeding0.1480.0020.151
model.matrix0.0970.0020.099
nIndividual0.0250.0010.025
pedigree0.0360.0020.039
prune0.0930.0030.097
relationshipAdditive0.1580.0030.161
removeIndividual0.0340.0020.035
sort.pedigree0.0530.0040.058
summary.pedigree0.0130.0010.013