Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 197/462HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: GGtools
Version: 3.11.18
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings GGtools_3.11.18.tar.gz
StartedAt: 2011-05-09 17:19:58 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 17:30:23 -0700 (Mon, 09 May 2011)
EllapsedTime: 625.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: GGtools.Rcheck
Warnings: NA

Command output

* 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

GGtools.Rcheck/00install.out:

* 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)

GGtools.Rcheck/GGtools-Ex.timings:

nameusersystemelapsed
X2chunk000
cisProxScores-class000
cisProxScores52.41 0.8254.05
clipPCs64.54 0.8665.72
degnerASE01000
eqtlTests12.66 0.1213.67
eqtlTestsManager-class000
ex60.060.000.06