encoDnaseI 0.1.6
VJ Carey
| Snapshot Date: 2010-11-12 00:25:07 -0800 (Fri, 12 Nov 2010) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/encoDnaseI | | Last Changed Rev: 1342 / Revision: 1384 | | Last Changed Date: 2010-10-13 18:21:56 -0700 (Wed, 13 Oct 2010) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.8-data-experiment/meat/encoDnaseI.Rcheck'
* using R version 2.13.0 Under development (unstable) (2010-11-10 r53547)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'encoDnaseI/DESCRIPTION' ... OK
* this is package 'encoDnaseI' version '0.1.6'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'encoDnaseI' 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ...Warning: running command '"E:\biocbld\bbs-2.8-bioc\R/bin/i386/Rterm.exe" R_DEFAULT_PACKAGES= --vanilla --slave -f E:\biocbld\bbs-2.8-data-experiment\tmpdir\RtmpdJDD9f\Rin7f651d4' had status 1
NOTE
Warning: non-unique value when setting 'row.names': 'new'
Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "new", "new" :
duplicate 'row.names' are not allowed
Calls: <Anonymous> ... rownames<- -> row.names<- -> row.names<-.data.frame
Execution halted
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'encoDnaseI' ...
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: GGBase
Loading required package: snpMatrix2
Loading required package: survival
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from 'package:Biobase':
updateObject
The following object(s) are masked from 'package:base':
Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, table
Loading required package: rtracklayer
Loading required package: RCurl
Loading required package: bitops
Loading required package: org.Hs.eg.db
Loading required package: GenomicRanges
Loading required package: ff
Loading required package: tools
Loading required package: bit
Loading package bit1.1-6
package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Attaching package: 'bit'
The following object(s) are masked from 'package:base':
xor
Loading package ff2.2-1
- getOption("fftempdir")=="E:/biocbld/bbs-2.8-data-experiment/tmpdir/RtmpjgkyWy"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16095641.6 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system
Attaching package ff
Attaching package: 'ff'
The following object(s) are masked from 'package:utils':
write.csv, write.csv2
The following object(s) are masked from 'package:base':
is.factor, is.ordered
Attaching package: 'snpMatrix'
The following object(s) are masked from 'package:snpMatrix2':
Fst, chi.squared, col.summary, deg.freedom, effect.sign,
effective.sample.size, filter.rules, glm.test.control,
imputation.maf, imputation.nsnp, imputation.r2, impute.snps,
misinherits, p.value, pool, pool2, qq.chisq, read.plink,
read.snps.long, row.summary, sample.size, single.snp.tests,
snp.cbind, snp.cor, snp.imputation, snp.lhs.estimates,
snp.lhs.tests, snp.post.multiply, snp.pre.multiply, snp.rbind,
snp.rhs.estimates, snp.rhs.tests, switch.alleles, tdt.snp,
test.allele.switch, write.snp.matrix, xxt
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (encoDnaseI)