GGtools 3.11.31
Vince Carey
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools | | Last Changed Rev: 56132 / Revision: 56603 | | Last Changed Date: 2011-06-13 03:37:12 -0700 (Mon, 13 Jun 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ ERROR ] | ERROR |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GGtools.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '3.11.31'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: multicore
* checking if this is a source package ... OK
* checking whether package 'GGtools' can be installed ... OK
* checking installed package size ... NOTE
installed size is 67.3Mb
sub-directories of 1Mb or more:
browserTrack 1.8Mb
data 49.6Mb
doc 10.5Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
ieqtlTests: no visible global function definition for 'mclapply'
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 ... NOTE
Note: significantly better compression could be obtained
by using tools::resaveRdaFiles() or R CMD build --resave-data
old_size new_size compress
ex6.rda 102Kb 52Kb xz
hmceuB36.2021.rda 34.2Mb 22.5Mb xz
m20.rda 3.5Mb 2.5Mb xz
strMultPop.rda 759Kb 435Kb xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... ERROR
Running examples in 'GGtools-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clipPCs
> ### Title: simple approach to removal of principal components from smlSet
> ### Aliases: clipPCs
> ### Keywords: models
>
> ### ** Examples
>
> data(hmceuB36.2021)
> library(illuminaHumanv1.db)
> g20 = get("20", revmap(illuminaHumanv1CHR))
> g20 = intersect(g20, featureNames(hmceuB36.2021))[1:25]
> hmc = clipPCs(hmceuB36.2021, 1:4)
> hmc = hmc[probeId(g20),]
> pcs = prcomp(t(exprs(hmceuB36.2021)))$x
> hmr = hmceuB36.2021[ probeId(g20), ]
> pData(hmr) = data.frame(pData(hmr), pcs[,1:4])
> hmc
SnpMatrix-based genotype set:
number of samples: 90
number of chromosomes present: 2
annotation: illuminaHumanv1.db
Expression data dims: 25 x 90
Phenodata: An object of class "AnnotatedDataFrame"
sampleNames: NA06985 NA06991 ... NA12892 (90 total)
varLabels: famid persid ... male (7 total)
varMetadata: labelDescription
> f1 = eqtlTests(hmc[chrnum("20"),], ˜male, targdir="clipdem")
Error in ff(initdata = cbind(maf, mingtf), vmode = "short", dim = c(length(maf), :
bad argument initdata for existing file; initializing existing file is invalid
Calls: eqtlTests -> ffSnpSummary -> ff
Execution halted
install for i386
* 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/RtmpyIl1XR"
- 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")==37570478.08 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system
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
add DLL for x64
* installing *source* package 'GGtools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGtools' as GGtools_3.11.31.zip
* DONE (GGtools)