GeneticsBase 1.2.0
Gregory Warnes
| Snapshot Date: 2008-04-02 12:12:36 -0700 (Wed, 02 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/GeneticsBase | | Last Changed Rev: 27709 / Revision: 30807 | | Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.2.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneticsBase' can be installed ... 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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 ... OK
* creating GeneticsBase-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/GeneticsBase.Rcheck/tests'
Running 'ExampleScript001.R'
Running 'test.R'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/GeneticsBase.Rcheck/tests'
OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneticsBase-manual.tex ... OK
* checking GeneticsBase-manual.tex ... OK
installing R.css in D:/biocbld/bbs-2.1-bioc/meat/GeneticsBase.Rcheck
---------- Making package GeneticsBase ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making LdMax.d from LdMax.cpp
making convert.d from convert.cpp
making getLDdist.d from getLDdist.cpp
making readGenes.ped.d from readGenes.ped.cpp
making register.d from register.cpp
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c LdMax.cpp -o LdMax.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c convert.cpp -o convert.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c register.cpp -o register.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include -i GeneticsBase_res.rc -o GeneticsBase_res.o
g++-sjlj -shared -s -o GeneticsBase.dll GeneticsBase.def LdMax.o convert.o getLDdist.o readGenes.ped.o register.o GeneticsBase_res.o -Ld:/biocbld/bbs-2.1-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package GeneticsBase for lazy loading
Loading required package: combinat
Attaching package: 'combinat'
The following object(s) are masked from package:utils :
combn
Loading required package: xtable
Loading required package: mvtnorm
Loading required package: haplo.stats
installing man source files
installing indices
Loading required package: methods
Loading required package: combinat
Attaching package: 'combinat'
The following object(s) are masked from package:utils :
combn
Loading required package: xtable
Loading required package: mvtnorm
Loading required package: haplo.stats
not zipping data
installing help
>>> Building/Updating help pages for package 'GeneticsBase'
Formats: text html latex example chm
ALZH text html latex example chm
Armitage text html latex example chm
CAMP text html latex example chm
HWE text html latex example chm
HWE.chisq text html latex example chm
HWE.exact text html latex example chm
LD-class text html latex example chm
LD text html latex example chm
LDband-class text html latex example chm
LDdist-class text html latex chm
PGtables text html latex example chm
PerlgenExample text html latex example chm
PfizerExample text html latex example chm
alleleCount text html latex example chm
alleleLevels text html latex example chm
alleleSummary text html latex example chm
alleles text html latex example chm
binsearch text html latex example chm
callCodes text html latex example chm
ci.balance text html latex example chm
convert text html latex example chm
decodeCallCodes text html latex example chm
desMarkers text html latex example chm
description text html latex example chm
diseq text html latex example chm
errorMetrics text html latex example chm
extractAlleles text html latex example chm
fastGrid text html latex example chm
founderGeneSet text html latex example chm
geneSet-class text html latex example chm
geneSet2Ped text html latex example chm
genotypeCoding text html latex example chm
genotypeLevels text html latex example chm
genotypeSummary text html latex example chm
genotypes text html latex example chm
gregorius text html latex example chm
haplo.em.w text html latex example chm
haplo.scan.w text html latex example chm
haplo.score.slide.w text html latex example chm
haplo.score.w text html latex example chm
hapmapchr text html latex example chm
homozygote text html latex example chm
html text html latex example chm
left text html latex example chm
makeMarkerInfo text html latex example chm
makeTransTable text html latex example chm
makeTransTableList text html latex example chm
markerInfo text html latex example chm
markerNames text html latex example chm
markerSummary text html latex example chm
missingCodes text html latex example chm
nallele text html latex example chm
nmarker text html latex example chm
notes text html latex example chm
ped2geneSet text html latex chm
phase text html latex example chm
ploidy text html latex example chm
print.LD text html latex example chm
qtlex text html latex example chm
read.pfizer text html latex example chm
read.phe text html latex example chm
readGenes text html latex example chm
readGenes.ped text html latex example chm
readGenes.perlegen text html latex example chm
readGenes.pfizer text html latex example chm
sampleInfo text html latex example chm
studyInfo text html latex example chm
transTables text html latex example chm
xbat text html latex example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "n;c:\Program Files\UltraEdit;c:\Program Files\Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\GeneticsBase.Rcheck\00_pkg_src\GeneticsBase\chm\GeneticsBase.chm
HHC4016: Warning: Cannot open "n;c:\Program Files\UltraEdit;c:\Program Files\Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL".
The following files were not compiled:
adding MD5 sums
* DONE (GeneticsBase)