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| Package 77/214 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
GeneticsBase1.0.0Gregory WarnesLast Changed Date: 2007-04-24 11:21:48 -0700 Last Changed Rev: 24214 | lamb1 | Linux (SUSE 10.1) | x86_64 | ERROR | skipped | |
| wellington | Linux (SUSE 9.2) | i686 | [ ERROR ] | skipped | ||
| lemming | Windows Server 2003 (32-bit) | x64 | ERROR | skipped | skipped |
| Package: GeneticsBase |
| Version: 1.0.0 |
| Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD build GeneticsBase |
| RetCode: 1 |
| Time: 49.8 seconds |
| Status: ERROR |
| PackageFile: None |
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* preparing 'GeneticsBase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'GeneticsBase' ...
** libs
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c convert.cpp -o convert.o
convert.cpp:1:2: warning: #import is obsolete, use an #ifndef wrapper in the header file
convert.cpp: In function `SEXPREC* convert2(SEXPREC*, SEXPREC*, SEXPREC*)':
convert.cpp:6: warning: unused variable `int maxlen'
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c LdMax.cpp -o LdMax.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
readGenes.ped.cpp: In function `int countLines(FILE*, int, int)':
readGenes.ped.cpp:86: warning: `int tmpnc2' might be used uninitialized in this
function
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c register.cpp -o register.o
g++ -shared -L/usr/local/lib -o GeneticsBase.so convert.o getLDdist.o LdMax.o readGenes.ped.o register.o -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** data
** inst
** save image
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
** help
>>> Building/Updating help pages for package 'GeneticsBase'
Formats: text html latex example
ALZH text html latex example
CAMP text html latex example
HWE text html latex example
HWE.chisq text html latex example
HWE.exact text html latex example
LD-class text html latex example
LD text html latex example
LDband-class text html latex example
LDdist-class text html latex
PGtables text html latex example
PerlgenExample text html latex example
PfizerExample text html latex example
alleleCount text html latex example
alleleLevels text html latex example
alleleSummary text html latex example
alleles text html latex example
binsearch text html latex example
callCodes text html latex example
ci.balance text html latex example
convert text html latex example
decodeCallCodes text html latex example
desMarkers text html latex example
description text html latex example
diseq text html latex example
errorMetrics text html latex example
extractAlleles text html latex example
fastGrid text html latex example
founderGeneSet text html latex example
geneSet-class text html latex example
genotypeLevels text html latex example
genotypeSummary text html latex example
genotypes text html latex example
gregorius text html latex example
haplo.em.w text html latex example
haplo.scan.w text html latex example
haplo.score.slide.w text html latex example
haplo.score.w text html latex example
hapmapchr text html latex example
homozygote text html latex example
html text html latex example
left text html latex example
makeMarkerInfo text html latex example
makeTransTable text html latex example
makeTransTableList text html latex example
markerInfo text html latex example
markerNames text html latex example
markerSummary text html latex example
missingCodes text html latex example
nallele text html latex example
nmarker text html latex example
notes text html latex example
ped2geneSet text html latex
phase text html latex example
ploidy text html latex example
power.casectl text html latex example
print.LD text html latex example
qtlex text html latex example
read.pfizer text html latex example
read.phe text html latex example
readGenes text html latex example
readGenes.ped text html latex example
readGenes.perlegen text html latex example
readGenes.pfizer text html latex example
sampleInfo text html latex example
studyInfo text html latex example
transTables text html latex example
xbat text html latex example
** building package 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
* DONE (GeneticsBase)
* creating vignettes ... ERROR
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
Error: processing vignette 'SummaryTables.Rnw' failed with diagnostics:
chunk 23
Error in write.GeneticsBaseSummary(x = x, filename = filename, ..., format = "latex") :
could not find function "print.xtable"
In addition: There were 15 warnings (use warnings() to see them)
Execution halted