BioC 3.3: CHECK report for GeneticsPed on linux2.bioconductor.org
This page was generated on 2015-10-27 12:11:35 -0400 (Tue, 27 Oct 2015).
GeneticsPed 1.33.0
David Henderson
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsPed | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
Summary
| Package: GeneticsPed |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GeneticsPed_1.33.0.tar.gz |
| StartedAt: 2015-10-27 04:10:25 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 04:10:51 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 26.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneticsPed.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GeneticsPed_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GeneticsPed.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.33.0’
* 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 ... [9s/9s] 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 ... 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 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’ [1s/1s]
[1s/1s] 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: OK
GeneticsPed.Rcheck/00install.out:
* installing *source* package ‘GeneticsPed’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ainverse.cc -o ainverse.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c eibd.cc -o eibd.o
gfortran -fpic -g -O2 -c ggmatmult.f -o ggmatmult.o
gfortran -fpic -g -O2 -c gpi.f -o gpi.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inbreed.cc -o inbreed.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inverseAdditive.cc -o inverseAdditive.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c meuwissen.cc -o meuwissen.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pedSort.cc -o pedSort.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pedtemplate.cc -o pedtemplate.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c register.cc -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sargolzaei.c -o sargolzaei.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sortped.cc -o sortped.o
g++ -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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:
| name | user | system | elapsed
|
| TDT | 0.170 | 0.016 | 0.188 |
|
| check | 0.05 | 0.00 | 0.05 |
|
| datasets | 0.01 | 0.00 | 0.01 |
|
| extend | 0.064 | 0.000 | 0.064 |
|
| family | 0.016 | 0.000 | 0.016 |
|
| founder | 0.003 | 0.000 | 0.003 |
|
| geneContribution | 0.04 | 0.00 | 0.04 |
|
| generatePedigree | 0.022 | 0.020 | 0.042 |
|
| generation | 0.021 | 0.001 | 0.024 |
|
| gpi | 0.008 | 0.000 | 0.008 |
|
| gpiUtil | 0.206 | 0.028 | 0.233 |
|
| inbreeding | 0.064 | 0.000 | 0.064 |
|
| model.matrix | 0.008 | 0.000 | 0.007 |
|
| nIndividual | 0.002 | 0.000 | 0.002 |
|
| pedigree | 0.003 | 0.000 | 0.004 |
|
| prune | 0.024 | 0.000 | 0.025 |
|
| relationshipAdditive | 0.076 | 0.000 | 0.076 |
|
| removeIndividual | 0.014 | 0.000 | 0.013 |
|
| sort.pedigree | 0.020 | 0.000 | 0.019 |
|
| summary.pedigree | 0.004 | 0.000 | 0.004 |
|