GGtools 3.11.18
Vince Carey
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools | | Last Changed Rev: 55337 / Revision: 55359 | | Last Changed Date: 2011-05-08 18:55:28 -0700 (Sun, 08 May 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ ERROR ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GGtools.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '3.11.18'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
'multicore' 'GGdata'
* checking if this is a source package ... OK
* checking whether package 'GGtools' can be installed ... OK
* checking installed package size ... NOTE
installed size is 67.9Mb
sub-directories of 1Mb or more:
browserTrack 1.8Mb
data 49.6Mb
doc 11.2Mb
GGEXsite 1.0Mb
pup 2.0Mb
* 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 ... NOTE
topKfeats: no visible binding for global variable 'i1'
topKfeats: no visible binding for global variable 'i2'
* checking Rd files ... NOTE
prepare_Rd: transScores.Rd:84-86: Dropping empty section \details
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'GGtools-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sm2ped
> ### Title: create a data.frame representing a PED file (MACH) from a
> ### SnpMatrix instance
> ### Aliases: sm2ped
> ### Keywords: models
>
> ### ** Examples
>
> library(snpStats)
> sm = chopsticks::read.HapMap.data(paste("file://",
+ system.file("hapmap/smallc20CEU.txt.gz", package="GGtools"), sep=""))
read header failed
conversion failed
temp file left at D:\biocbld\bbs-2.9-bioc\tmpdir\RtmpHNwRwU\file629332d9 for retrying conversion locally with url file://
> supp = sm[[2]]
> smat = sm[[1]]
> reldata = read.table(system.file("hapmap/relationships_w_pops_051208.txt",
+ package="GGtools"), header=TRUE)
> rownames(reldata) = as.character(reldata[,2])
> hids = rownames(smat)
> hrel = reldata[hids,]
> hrel[1:5,]
FID IID dad mom sex pheno population
NA <NA> <NA> <NA> <NA> NA NA <NA>
NA.1 <NA> <NA> <NA> <NA> NA NA <NA>
NA.2 <NA> <NA> <NA> <NA> NA NA <NA>
NA.3 <NA> <NA> <NA> <NA> NA NA <NA>
NA.4 <NA> <NA> <NA> <NA> NA NA <NA>
> args(sm2ped)
function (sm, snpsupp, missing.code = "N", family, person, father,
mother, sex)
NULL
> ac = as.character
> ss = sm2ped(smat, supp, fam=ac(hrel[,1]), person=ac(hrel[,2]), father=ac(hrel[,3]),
+ mother=ac(hrel[,4]), sex=hrel[,5])
Error in if (nsnp != nsup) stop("number of snps in sm not equal to number of support lines") :
argument is of length zero
Calls: sm2ped -> whmu
Execution halted
* installing *source* package 'GGtools' ...
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: snpStats
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'Matrix'
The following object(s) are masked from 'package:base':
det
Loading required package: RSQLite
Loading required package: DBI
Loading required package: AnnotationDbi
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, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: RCurl
Loading required package: bitops
Loading package bit1.1-7
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
Loading package ff2.2-2
- getOption("fftempdir")=="D:/biocbld/bbs-2.9-bioc/tmpdir/Rtmp0YxGnw"
- 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")==42928701.44 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==2146435072 -- consider a different value for tuning your system
in method for 'min_p_vals' with signature '"maxchisq","character","character","numeric"': no definition for class "maxchisq"
in method for 'coerce' with signature '"multffManager","eqtlTestsManager"': no definition for class "multffManager"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'GGtools_2011.Rnw'
'binf09supp.Rnw'
'external.Rnw'
** testing if installed package can be loaded
* DONE (GGtools)