From hamid.khalili at gmail.com  Thu Apr 29 17:39:25 2010
From: hamid.khalili at gmail.com (Hamid Khalili)
Date: Thu, 29 Apr 2010 17:39:25 +0200
Subject: [Rd] R CMD check Error after R CMD build for R-2.11.0
Message-ID: <v2hb1c1eb501004290839m41c0bf5mac8c3ebd75ab7add@mail.gmail.com>

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.
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,

-- 
Hamid Khalili



[Rd] R CMD check Error after R CMD build for R-2.11.0
Hamid Khalili