GGtools 3.8.4
Vince Carey
| Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/GGtools | | Last Changed Rev: 51512 / Revision: 54588 | | Last Changed Date: 2010-12-13 12:32:55 -0800 (Mon, 13 Dec 2010) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ ERROR ] | OK |
* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/GGtools.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '3.8.4'
* 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 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
bestCis: no visible binding for '<<-' assignment to 'maxgap'
bestCis: no visible global function definition for 'mclapply'
diagffCC: no visible global function definition for 'mclapply'
diagffCC : <anonymous>: no visible binding for '<<-' assignment to 'ex'
eqtlTests: no visible global function definition for 'mclapply'
eqtlTestsMACH : <anonymous> : <anonymous>: no visible global function
definition for 'snp.rhs.testsMACH'
maxchisq: no visible global function definition for 'mclapply'
sumScores2ff: no visible global function definition for 'mclapply'
sumScores2ff : <anonymous>: no visible binding for '<<-' assignment to
'ex'
min_p_vals,maxchisq-character-character-numeric : mtcorrp: no visible
global function definition for 'mt.rawp2adjp'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package(s) unavailable to check Rd xrefs: 'multicore'
* 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 ... ERROR
Running examples in 'GGtools-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scoresInRanges
> ### Title: structured survey of eqtlTestsManager to retrieve scores cis to
> ### genes
> ### Aliases: scoresInRanges
> ### Keywords: models
>
> ### ** Examples
>
> gl = GGtools:::geneLimits( anno="illuminaHumanv1.db" )
Loading required package: illuminaHumanv1.db
> egl = GGtools:::extendGR(gl, siz=5e5)
> data(hmceuB36.2021)
> gl20 = names(egl[ which(seqnames(egl) == "chr20") ] )[1:20]
> p2 = intersect( gl20, featureNames(hmceuB36.2021) )
> curd = getwd()
> setwd(tempdir())
> if (file.exists("foo"))system("rm -rf foo")
> ee = eqtlTests( hmceuB36.2021[ probeId(p2), ], ˜1, targdir="sir" )
> library(ceu1kg)
> data(ceu1kgMeta_20)
Warning in data(ceu1kgMeta_20) : data set 'ceu1kgMeta_20' not found
> ceu1kgMeta_20 = updateObject(ceu1kgMeta_20)
Execution halted
* installing *source* package 'GGtools' ...
** 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: snpMatrix
Loading required package: survival
Loading required package: splines
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, mapply, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, table
Loading required package: RCurl
Loading required package: bitops
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")=="D:/biocbld/bbs-2.7-bioc/tmpdir/RtmpwJ3hAb"
- 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
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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (GGtools)