GeneticsPed 1.26.0
David Henderson
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GeneticsPed | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf GeneticsPed.buildbin-libdir && mkdir GeneticsPed.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneticsPed.buildbin-libdir GeneticsPed_1.26.0.tar.gz >GeneticsPed-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GeneticsPed.buildbin-libdir --install="check:GeneticsPed-install.out" --force-multiarch --no-vignettes --timings GeneticsPed_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/GeneticsPed.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.26.0'
* 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 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 ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Packages in Depends field not imported from:
'MASS' 'gdata' 'genetics'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'checkAttributes' 'dropLevels' 'unusedLevels'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-2.14-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/i386/GeneticsPed.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.14-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/x64/GeneticsPed.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'doRUnit.R' [1s]
[2s] OK
** running tests for arch 'x64' ...
Running 'doRUnit.R' [2s]
[2s] 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
NOTE: There were 5 notes.
See
'E:/biocbld/bbs-2.14-bioc/meat/GeneticsPed.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GeneticsPed' ...
** libs
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ainverse.cc -o ainverse.o
ainverse.cc: In function 'void SetColumns(EIBDMat&)':
ainverse.cc:66:18: warning: variable 'cindex' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c eibd.cc -o eibd.o
gfortran -m32 -O3 -mtune=core2 -c ggmatmult.f -o ggmatmult.o
gfortran -m32 -O3 -mtune=core2 -c gpi.f -o gpi.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c inbreed.cc -o inbreed.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c inverseAdditive.cc -o inverseAdditive.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c meuwissen.cc -o meuwissen.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pedSort.cc -o pedSort.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pedtemplate.cc -o pedtemplate.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c register.cc -o register.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sargolzaei.c -o sargolzaei.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c sortped.cc -o sortped.o
sortped.cc: In function 'void SortPed(Pedigree&, TPedVec&)':
sortped.cc:5:8: warning: variable 'ancestor' set but not used [-Wunused-but-set-variable]
g++ -m32 -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 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -lgfortran -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'GeneticsPed' ...
** libs
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ainverse.cc -o ainverse.o
ainverse.cc: In function 'void SetColumns(EIBDMat&)':
ainverse.cc:66:18: warning: variable 'cindex' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c eibd.cc -o eibd.o
gfortran -m64 -O2 -mtune=core2 -c ggmatmult.f -o ggmatmult.o
gfortran -m64 -O2 -mtune=core2 -c gpi.f -o gpi.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c inbreed.cc -o inbreed.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c inverseAdditive.cc -o inverseAdditive.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c meuwissen.cc -o meuwissen.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pedSort.cc -o pedSort.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pedtemplate.cc -o pedtemplate.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c register.cc -o register.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sargolzaei.c -o sargolzaei.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c sortped.cc -o sortped.o
sortped.cc: In function 'void SortPed(Pedigree&, TPedVec&)':
sortped.cc:5:8: warning: variable 'ancestor' set but not used [-Wunused-but-set-variable]
g++ -m64 -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 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -lgfortran -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneticsPed' as GeneticsPed_1.26.0.zip
* DONE (GeneticsPed)