[Bioc-devel] Flagme creating vignettes ERROR

[Riccardo Romoli]

Hi, last night I received an automatic message regardless the flagme 
package (I'm the co-author and the manteiner):

   o ERROR for 'R CMD build' on zin2. See the details here:
 
http://bioconductor.org/checkResults/3.1/bioc-LATEST/flagme/zin2-buildsrc.html

I followed the link above and I see the error:

%----------------------------------------------------------------------------%
##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build --keep-empty-dirs 
--no-resave-data flagme
###
##############################################################################
##############################################################################


* checking for file ‘flagme/DESCRIPTION’ ... OK
* preparing ‘flagme’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR

...

Error: processing vignette 'flagme.Rnw' failed with diagnostics:
  chunk 3 (label = addXCMS)
Error in x$membership : $ operator not defined for this S4 class
Execution halted
%---------------------------------------------------------------------------------%


I downloaded the source of the package and I tried to build it. I get no 
errors.


%---------------------------------------------------------------------------------%
:~$ R CMD build --keep-empty-dirs --no-resave-data flagme

* checking for file ‘flagme/DESCRIPTION’ ... OK
* preparing ‘flagme’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘flagme_1.24.0.tar.gz’
%----------------------------------------------------------------------------------%


What should I do?

All the best, Riccardo


-- 
Riccardo Romoli, PhD
Mass Spectrometry Centre - CISM
University of Florence
Via Ugo Schiff 6, 50019 Sesto Fiorentino (FI), Italy
Phone: +39 055 4573783/2
email: riccardo.romoli at unifi.it
web site: www.cism.unifi.it