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 'D:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-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 ... WARNING
Found the following significant warnings:
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
See 'D:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck/00install.out' for details.
* 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
WARNING: There was 1 warning, see
'D:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck/00check.log'
for details
* installing *source* package 'GeneticsPed' ...
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c ainverse.cc -o ainverse.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c eibd.cc -o eibd.o
x86_64-w64-mingw32-gfortran -O2 -mtune=core2 -c ggmatmult.f -o ggmatmult.o
x86_64-w64-mingw32-gfortran -O2 -mtune=core2 -c gpi.f -o gpi.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c inbreed.cc -o inbreed.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c inverseAdditive.cc -o inverseAdditive.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c meuwissen.cc -o meuwissen.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c pedSort.cc -o pedSort.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c pedtemplate.cc -o pedtemplate.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c register.cc -o register.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sargolzaei.c -o sargolzaei.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c sortped.cc -o sortped.o
x86_64-w64-mingw32-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 -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/libs/x64
** R
** data
** inst
** preparing package for lazy loading
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
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
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
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.
Warning messages:
1: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
2: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
* DONE (GeneticsPed)