[Rd] R CMD check Error after R CMD build for R-2.11.0
Hamid Khalili
hamid.khalili at gmail.com
Thu Apr 29 17:39:25 CEST 2010
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
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