From ligges at statistik.tu-dortmund.de  Thu Apr 29 19:13:54 2010
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Thu, 29 Apr 2010 19:13:54 +0200
Subject: [Rd] R CMD check Error after R CMD build for R-2.11.0
In-Reply-To: <v2hb1c1eb501004290839m41c0bf5mac8c3ebd75ab7add@mail.gmail.com>
References: <v2hb1c1eb501004290839m41c0bf5mac8c3ebd75ab7add@mail.gmail.com>
Message-ID: <4BD9BE52.7050507@statistik.tu-dortmund.de>



On 29.04.2010 17:39, Hamid Khalili wrote:
> Dear UseR,
>
> I get an error when I run "R CMD check" on my .tar.gz file package,
> and I don't  understand why since I don't obtain any error with "R CMD
> check" on the package directory. Do you have any idea ?
>
> $ sudo ./R-2.11.0/bin/R CMD check eqtl_1.1.tar.gz
>
> and
>
> $ sudo ./R-2.11.0/bin/R CMD --check-subdirs=no eqtl_1.1.tar.gz
>
> return an Error
>
> * checking for working pdflatex ... OK
> * using log directory '/home/hkhalili/Desktop/eqtl.Rcheck'
> * using R version 2.11.0 (2010-04-22)
> * using session charset: UTF-8
> * checking for file 'eqtl/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'eqtl' version '1.1'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking for executable files ... OK
> * checking whether package 'eqtl' can be installed ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... 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 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 data for non-ASCII characters ... OK
> * checking examples ... ERROR
> Running examples in 'eqtl-Ex.R' failed.
> The error most likely occurred in:
>
>> ### * Rsq.2.array
>>
>> flush(stderr()); flush(stdout())
>>
>> ### Name: Rsq.2.array
>> ### Title: Add R square data to peak.array data frame
>> ### Aliases: Rsq.2.array
>>
>> ### ** Examples
>>
>> data(seed10);
>>
>> # Genome scan and QTL detection
>> out.em<- scanone(seed10, pheno.col=1:50, model='normal', method='em');
> Warning in checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :
>    Dropping 263 individuals with missing phenotypes.
>
> Warning in checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :
>    Dropping 263 individuals with missing phenotypes.
>
> Warning in checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :
>    Dropping 263 individuals with missing phenotypes.
>
>> out.peak<- define.peak(out.em, 'all');
> Error: could not find function "define.peak"
> Execution halted
>
> The Warnings in checkcovar are normal warnings (from the required
> package 'qtl'). The function "define.peak" is part of the package I'm
> checking (eqtl) and its Rd and R files are checked before
> "Rsq.2.array" function without any Error.

Are you sure about the spelling? Do you have a namespace and forgot to 
export?

Uwe Ligges


> The functions' example running the same commands line with define.peak
> didn't return any Error.
>
> $ sudo ./R-2.11.0/bin/R CMD  check --check-subdirs=yes eqtl
>
> and
>
> $ sudo ./R-2.11.0/bin/R CMD check eqtl/
>
> return no error
>
> * checking for working pdflatex ... OK
> * using log directory '/home/hkhalili/Desktop/eqtl.Rcheck'
> * using R version 2.11.0 (2010-04-22)
> * using session charset: UTF-8
> * checking for file 'eqtl/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'eqtl' version '1.1'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking for executable files ... OK
> * checking whether package 'eqtl' can be installed ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... 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 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 ... OK
> * 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 data for non-ASCII characters ... OK
> * checking examples ... OK
> * checking PDF version of manual ... OK
>
> $ ./R-2.11.0/bin/R CMD build /media/HAMID/eqtl
> * checking for file '/media/HAMID/eqtl/DESCRIPTION' ... OK
> * preparing '/media/HAMID/eqtl':
> * checking DESCRIPTION meta-information ... OK
> * removing junk files
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building 'eqtl_1.1.tar.gz'
>
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
>   [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=fr_FR.UTF-8
>   [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>> version
>                 _
> platform       x86_64-unknown-linux-gnu
> arch           x86_64
> os             linux-gnu
> system         x86_64, linux-gnu
> status
> major          2
> minor          11.0
> year           2010
> month          04
> day            22
> svn rev        51801
> language       R
> version.string R version 2.11.0 (2010-04-22)
>
> $ ll /media/HAMID/eqtl/man/
> total 100
> -rwx------ 1 hkhalili hkhalili 17244 2010-04-29 12:21 AA.brief.introduction.Rd
> -rwx------ 1 hkhalili hkhalili  3076 2010-04-28 17:21 A.importing.data.Rd
> -rwx------ 1 hkhalili hkhalili  1789 2010-04-28 17:21 ATH.coord.Rd
> -rwx------ 1 hkhalili hkhalili  1107 2010-04-29 12:22 BSpgmap.Rd
> -rwx------ 1 hkhalili hkhalili  3314 2010-04-29 11:32 calc.adef.Rd
> -rwx------ 1 hkhalili hkhalili  3496 2010-04-28 17:21 calc.Rsq.Rd
> -rwx------ 1 hkhalili hkhalili  1848 2010-04-28 17:21 cim.peak.Rd
> -rwx------ 1 hkhalili hkhalili  4630 2010-04-29 13:04 classify.qtl.Rd
> -rwx------ 1 hkhalili hkhalili  2136 2010-04-29 11:27 cleanphe.Rd
> -rwx------ 1 hkhalili hkhalili  1684 2010-04-28 17:21 cover.peak.Rd
> -rwx------ 1 hkhalili hkhalili  8680 2010-04-29 13:54 define.peak.Rd
> -rwx------ 1 hkhalili hkhalili  1654 2010-04-28 17:21 drop.peakfeat.Rd
> -rwx------ 1 hkhalili hkhalili   403 2010-04-28 17:21 eqtlversion.Rd
> -rwx------ 1 hkhalili hkhalili  4260 2010-04-28 17:21 genoplot.Rd
> -rwx------ 1 hkhalili hkhalili  2117 2010-04-28 17:21 gpt.Rd
> -rwx------ 1 hkhalili hkhalili  3401 2010-04-28 17:21 localize.qtl.Rd
> -rwx------ 1 hkhalili hkhalili  1177 2010-04-29 11:31 map.peak.Rd
> -rwx------ 1 hkhalili hkhalili   782 2010-04-28 17:21 mnames.map.Rd
> -rwx------ 1 hkhalili hkhalili  3123 2010-04-28 17:21 peak.2.array.Rd
> -rwx------ 1 hkhalili hkhalili  2219 2010-04-28 17:21 peaksummary.Rd
> -rwx------ 1 hkhalili hkhalili  1404 2010-04-28 17:21 plotRsq.Rd
> -rwx------ 1 hkhalili hkhalili   979 2010-04-28 17:21 pseudo.map.Rd
> -rwx------ 1 hkhalili hkhalili  2072 2010-04-29 14:52 Rsq.2.array.Rd
> -rwx------ 1 hkhalili hkhalili  1354 2010-04-28 17:21 seed10.Rd
> -rwx------ 1 hkhalili hkhalili  1830 2010-04-28 17:21 wash.covar.Rd
>
> ll /media/HAMID/eqtl/r/
> total 90
> -rwx------ 1 hkhalili hkhalili  4239 2010-04-28 17:21 calc.adef.R
> -rwx------ 1 hkhalili hkhalili  4667 2010-04-28 17:21 calc.Rsq.R
> -rwx------ 1 hkhalili hkhalili  2848 2010-04-28 17:21 cim.peak.R
> -rwx------ 1 hkhalili hkhalili  4969 2010-04-28 17:21 classify.qtl.R
> -rwx------ 1 hkhalili hkhalili  1273 2010-04-28 17:21 cleanphe.r
> -rwx------ 1 hkhalili hkhalili  2579 2010-04-28 17:21 cover.peak.R
> -rwx------ 1 hkhalili hkhalili 11051 2010-04-28 17:21 define.peak.R
> -rwx------ 1 hkhalili hkhalili  1534 2010-04-28 17:21 drop.peakfeat.R
> -rwx------ 1 hkhalili hkhalili   104 2010-04-28 17:21 eqtlversion.R
> -rwx------ 1 hkhalili hkhalili  9538 2010-04-28 17:21 genoplot.r
> -rwx------ 1 hkhalili hkhalili  1872 2010-04-28 17:21 gpt.r
> -rwx------ 1 hkhalili hkhalili  5534 2010-04-28 17:21 localize.qtl.R
> -rwx------ 1 hkhalili hkhalili  1195 2010-04-28 17:21 map.peak.R
> -rwx------ 1 hkhalili hkhalili   827 2010-04-28 17:21 mnames.map.R
> -rwx------ 1 hkhalili hkhalili  1760 2010-04-28 17:21 peak.2.array.R
> -rwx------ 1 hkhalili hkhalili 11483 2010-04-28 17:21 peaksummary.R
> -rwx------ 1 hkhalili hkhalili  1659 2010-04-28 17:21 plotRsq.R
> -rwx------ 1 hkhalili hkhalili   928 2010-04-28 17:21 pseudo.map.R
> -rwx------ 1 hkhalili hkhalili  1841 2010-04-28 17:21 Rsq.2.array.R
> -rwx------ 1 hkhalili hkhalili  3790 2010-04-28 17:21 wash.covar.R
>
>
> Do you have any ideas in which direction I could search ?
>
> thanks a lot,
> sincerely,
>



[Rd] R CMD check Error after R CMD build for R-2.11.0
Uwe Ligges