From laurent at cbs.dtu.dk  Tue Mar 11 07:22:07 2003
From: laurent at cbs.dtu.dk (Laurent Gautier)
Date: Tue Mar 11 07:20:11 2003
Subject: [Rd] problem with R-devel and R CMD check ?
Message-ID: <20030311062207.GA272066@genome.cbs.dtu.dk>

Hi,

R CMD check is causing some "make sure it passes check, #@#$@%% !!
- I *did* check it passes check #$%#$!5 !!!" disagrement...

I currently have two versions of the same package... one goes through
the check, the other does not.

bin/R CMD check ~/these/R/affy --library=${HOME}/myRlib
does while
bin/R CMD check ~/these/R/affy-taniwha/affy --library=${HOME}/myRlib
does not

> diff -r --brief ~/these/R/affy-taniwha/affy/R ~/these/R/affy/R | grep -v '~$' | grep -v CVS
Only in /home/laurent/these/R/affy-taniwha/affy/R: bg.Affy.chipwide.R_back
Only in /home/laurent/these/R/affy-taniwha/affy/R: express.R_back
Only in /home/laurent/these/R/affy-taniwha/affy/R: normalize.qspline.R_back
Only in /home/laurent/these/R/affy/R: pairs.AffyBatch.R_exp
Only in /home/laurent/these/R/affy-taniwha/affy/R: read.affybatch.R_back
Only in /home/laurent/these/R/affy-taniwha/affy/R: rma.R_back
>


Any hint ?


L.

PS: the ouput of R check when failing is:
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking generic/method consistency ... WARNING
Error in .loadPackageQuietly(package, lib.loc) : 
        Error in .Last.lib(libpath) : Target of assignment expands to non-language object
Execution halted
* checking for assignment functions with final arg not named 'value' ... WARNING
Error in .loadPackageQuietly(package, lib.loc) : 
        Error in .Last.lib(libpath) : Target of assignment expands to non-language object
Execution halted
* checking Rd files ... OK
* checking for undocumented objects ... ERROR
Error in .loadPackageQuietly(package, lib.loc) :


[Rd] problem with R-devel and R CMD check ?
Laurent Gautier