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Package 164/419HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.12.0
David Henderson
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/GeneticsPed
Last Changed Rev: 50293 / Revision: 54588
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 

Summary

Package: GeneticsPed
Version: 1.12.0
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneticsPed_1.12.0.tar.gz
StartedAt: 2011-04-07 07:09:36 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 07:10:29 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 52.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GeneticsPed.Rcheck
Warnings: 7

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.12.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 'E:/biocbld/bbs-2.7-bioc/meat/GeneticsPed.Rcheck/00install.out' for details.
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
* 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 ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
* checking Rd \usage sections ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: gtools
* checking data for non-ASCII characters ... 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 examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: RUnit
* checking tests ...
  Running 'doRUnit.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 7 warnings, see
  'E:/biocbld/bbs-2.7-bioc/meat/GeneticsPed.Rcheck/00check.log'
for details

GeneticsPed.Rcheck/00install.out:

* installing *source* package 'GeneticsPed' ...
** libs
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c ainverse.cc -o ainverse.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c eibd.cc -o eibd.o
gfortran     -O3  -c ggmatmult.f -o ggmatmult.o
gfortran     -O3  -c gpi.f -o gpi.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c inbreed.cc -o inbreed.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c inverseAdditive.cc -o inverseAdditive.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c meuwissen.cc -o meuwissen.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c pedSort.cc -o pedSort.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c pedtemplate.cc -o pedtemplate.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c register.cc -o register.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c sargolzaei.c -o sargolzaei.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -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˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/libs/i386
** 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
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object(s) are masked from 'package:utils':

    object.size

Loading required package: combinat

Attaching package: 'combinat'

The following object(s) are masked from 'package:utils':

    combn

Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm

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.


Attaching package: 'genetics'

The following object(s) are masked from 'package:base':

    %in%, as.factor, order

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneticsPed)

GeneticsPed.Rcheck/GeneticsPed-Ex.timings:

nameusersystemelapsed
TDT0.050.000.08
check0.080.000.08
datasets0.030.000.03
extend0.220.000.22
family0.040.000.04
founder000
geneContribution0.130.000.12
generatePedigree0.120.000.13
generation0.100.000.09
gpi000
gpiUtil0.010.000.02
inbreeding0.060.000.07
model.matrix0.030.000.03
nIndividual000
pedigree0.020.000.01
prune0.060.000.07
relationshipAdditive0.080.020.14
removeIndividual0.030.000.03
sort.pedigree0.030.010.05
summary.pedigree000