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Package 203/514HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.16.0
David Henderson
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GeneticsPed
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: GeneticsPed
Version: 1.16.0
Command: rm -rf GeneticsPed.buildbin-libdir && mkdir GeneticsPed.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneticsPed.buildbin-libdir GeneticsPed_1.16.0.tar.gz >GeneticsPed-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=GeneticsPed.buildbin-libdir --install="check:GeneticsPed-install.out" --force-multiarch --no-vignettes --timings GeneticsPed_1.16.0.tar.gz && mv GeneticsPed.buildbin-libdir/* GeneticsPed.Rcheck/ && rmdir GeneticsPed.buildbin-libdir
StartedAt: 2012-03-24 01:28:40 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:29:56 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 75.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GeneticsPed.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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
* 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
* 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 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 ... WARNING
Unknown package(s) 'kinship' in Rd xrefs
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'RUnit'
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64'
  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

GeneticsPed.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneticsPed' ...
** libs
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/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++  -I"D:/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"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c inbreed.cc -o inbreed.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c inverseAdditive.cc -o inverseAdditive.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c meuwissen.cc -o meuwissen.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c pedSort.cc -o pedSort.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c pedtemplate.cc -o pedtemplate.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c register.cc -o register.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c sargolzaei.c -o sargolzaei.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/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++ -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/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.buildbin-libdir/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.


add DLL for x64

* installing *source* package 'GeneticsPed' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -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"D:/biocbld/BBS-2˜1.9-B/R/include"     -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"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c inbreed.cc -o inbreed.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c inverseAdditive.cc -o inverseAdditive.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c meuwissen.cc -o meuwissen.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pedSort.cc -o pedSort.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pedtemplate.cc -o pedtemplate.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c register.cc -o register.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sargolzaei.c -o sargolzaei.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -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 -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/x64
** 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.

* MD5 sums
packaged installation of 'GeneticsPed' as GeneticsPed_1.16.0.zip

* DONE (GeneticsPed)