GeneticsPed 1.16.0
David Henderson
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GeneticsPed | | Last Changed Rev: 59920 / Revision: 61898 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.16.0'
* 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 whether package 'GeneticsPed' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package(s) unavailable to check Rd xrefs: 'kinship'
* 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 ... NOTE
'library' or 'require' call not declared from: 'gtools'
* 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 examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'RUnit'
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'GeneticsPed' ...
** libs
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c ainverse.cc -o ainverse.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c eibd.cc -o eibd.o
gfortran -O3 -mtune=core2 -c ggmatmult.f -o ggmatmult.o
gfortran -O3 -mtune=core2 -c gpi.f -o gpi.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c inbreed.cc -o inbreed.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c inverseAdditive.cc -o inverseAdditive.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c meuwissen.cc -o meuwissen.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c pedSort.cc -o pedSort.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c pedtemplate.cc -o pedtemplate.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c register.cc -o register.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sargolzaei.c -o sargolzaei.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c sortped.cc -o sortped.o
g++ -shared -s -static-libgcc -o GeneticsPed.dll tmp.def 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 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/libs/i386
** R
** data
** inst
** preparing package for lazy loading
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'geneticRelatedness.Rnw'
'pedigreeHandling.Rnw'
'quanGenAnimalModel.Rnw'
** testing if installed package can be loaded
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
* DONE (GeneticsPed)