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