[Bioc-devel] Error on pitt (Mac OS X Tiger (10.4.11) / i386)

[Patrick Aboyoun]

Benedikt,
It looks like you have worked around the problem because Starr's build today on pitt was OK:

http://bioconductor.org/checkResults/2.5/bioc-LATEST/Starr/pitt-buildsrc.html

The main change you made was to switch from creating a png to a pdf graphics file for one of your plots. pitt (Mac OS X Tiger (10.4.11) / i386) has had some issues with png (bitmapped) graphics. After some experimentation on pitt, we have found that the cairo (instead of the standard default quartz) bitmap device is the most robust and we use cairo for all the bitmap graphics on pitt by setting

options(bitmapType = "cairo")

I'll set aside some time in the comming days to see if I can uncover why bitmapped graphics cause occasional problems on pitt.


Patrick



zacher at lmb.uni-muenchen.de wrote:
> Hello BioC-develers,
>
> I just contributed my first package (Starr) to bioconductor.
> I get an error on pitt (Mac OS X Tiger (10.4.11) / i386) at the
> multiple platform build/check report (shown below).
> On the other computers, no error occurs. As I don't use MAC 
> and the error only occurs on this machine, I have no idea how to 
> fix the problem. Is it a problem with the package, or with the machine?
> Best regards
>
> Benedikt
>
>
> -----------------------------------------------------------
>
> * checking for file 'Starr/DESCRIPTION' ... OK
> * preparing 'Starr':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to re-build vignettes
> * installing *source* package 'Starr' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: RColorBrewer
> Loading required package: limma
> Loading required package: Matrix
> Loading required package: lattice
>
> Attaching package: 'Matrix'
>
>
> 	The following object(s) are masked from package:base :
>
> 	 rcond 
>
> Loading required package: grid
> ** help
> *** installing help indices
> ** building package indices ...
> * DONE (Starr)
> * creating vignettes ... ERROR
> Loading required package: Ringo
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: RColorBrewer
> Loading required package: limma
> Loading required package: Matrix
> Loading required package: lattice
>
> Attaching package: 'Matrix'
>
>
> 	The following object(s) are masked from package:base :
>
> 	 rcond 
>
> Loading required package: grid
> Loading required package: affy
> Loading required package: affxparser
>
> Attaching package: 'Starr'
>
>
> 	The following object(s) are masked from package:affy :
>
> 	 plotDensity 
>
>
> 	The following object(s) are masked from package:limma :
>
> 	 plotMA 
>
>
> Error: processing vignette 'Starr.Rnw' failed with diagnostics:
>  chunk 43 (label=plotProfiles) 
> Error in grid.Call.graphics("L_setviewport", pvp, TRUE) : 
>   Non-finite location and/or size for viewport
> In addition: There were 50 or more warnings (use warnings() to see the first 50)
> Execution halted
>
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