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BioC 3.5: CHECK report for GeneticsPed on malbec2

This page was generated on 2017-08-16 13:12:50 -0400 (Wed, 16 Aug 2017).

Package 528/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneticsPed 1.38.1
David Henderson
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GeneticsPed
Last Changed Rev: 129423 / Revision: 131943
Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneticsPed
Version: 1.38.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GeneticsPed_1.38.1.tar.gz
StartedAt: 2017-08-15 23:19:10 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:19:43 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 32.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GeneticsPed_1.38.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GeneticsPed.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneticsPed/DESCRIPTION’ ... OK
* this is package ‘GeneticsPed’ version ‘1.38.1’
* 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 ... 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 loading without being on the library search path ... 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 ... NOTE
generatePedigree: no visible global function definition for ‘runif’
model.matrix.Pedigree: no visible global function definition for
  ‘model.matrix’
writeMendel: no visible global function definition for ‘?’
writeMendel: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  ? model.matrix runif write.csv
Consider adding
  importFrom("stats", "model.matrix", "runif")
  importFrom("utils", "?", "write.csv")
to your NAMESPACE file.
* 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 GNU extensions in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/GeneticsPed.Rcheck/00check.log’
for details.


GeneticsPed.Rcheck/00install.out:

* installing *source* package ‘GeneticsPed’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ainverse.cc -o ainverse.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c eibd.cc -o eibd.o
f95   -fpic  -g -O2  -Wall -c ggmatmult.f -o ggmatmult.o
f95   -fpic  -g -O2  -Wall -c gpi.f -o gpi.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c inbreed.cc -o inbreed.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c inverseAdditive.cc -o inverseAdditive.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c meuwissen.cc -o meuwissen.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pedSort.cc -o pedSort.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pedtemplate.cc -o pedtemplate.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.cc -o register.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sargolzaei.c -o sargolzaei.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sortped.cc -o sortped.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/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 -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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
TDT0.3080.0200.547
check0.1600.0000.156
datasets0.0120.0000.011
extend0.0360.0000.037
family0.0880.0000.085
founder0.0000.0000.003
geneContribution0.0640.0000.065
generatePedigree0.0240.0160.037
generation0.0600.0000.063
gpi0.0280.0040.047
gpiUtil0.3960.0160.436
inbreeding0.1160.0000.117
model.matrix0.0080.0000.009
nIndividual0.0040.0000.002
pedigree0.0040.0000.004
prune0.1120.0000.108
relationshipAdditive0.1120.0000.114
removeIndividual0.0360.0000.035
sort.pedigree0.0120.0000.012
summary.pedigree0.0040.0000.003