REDUCE Suite

Hi Xiang-Jun,

When I run these commands:

cd examples/MatrixREDUCE/spellman-alpha
sh commandline.sh
LogoGenerator -file=results/psam_001.xml -format=pdf

I get the following error:

GPL Ghostscript 9.19:

  ERROR:
    Can't set GraphicsAlphaBits or TextAlphaBits with a vector device.
Unrecoverable error: rangecheck in .putdeviceprops
system('gs -sOutputFile=./psam_001.pdf \
   -sDEVICE=pdfwrite \
   -dPDFSETTINGS=/printer \
   -dEmbedAllFonts=true \
   -dDEVICEWIDTHPOINTS=340 \
   -dDEVICEHEIGHTPOINTS=213 \
   -q -r96 -dTextAlphaBits=4 -dSAFER -dBATCH -dNOPAUSE \
   ./temp_logo.eps
') returns nonzero (65280)

The error seems to be triggered by the "-dTextAlphaBits=4" option. When I run "gs" manually without it, it work fine.

Seems that this is a known problem with more recent versions of "gs". I use version 9.19 on a Mac OS 10.11.6.

Thanks,
Harmen

Hi Xiang-Jun,

PDF support seems important to keep, and removing the option "-dTextAlphaBits=4" from config/pkg_settings.cfg completely solved the problem for me for this format, so I can continue with what I was doing now.

However, I agree that it will be best to discontinue GIF support. On my Mac at least, "convert" is not installed by default, and indeed GIF generation with "-format=gif" does not work:

$ LogoGenerator -file=results/psam_001.xml -format=gif
sh: line 6: convert: command not found
system('gs -sOutputFile=- \
   -sDEVICE=png16m \
   -dDEVICEWIDTHPOINTS=340 \
   -dDEVICEHEIGHTPOINTS=213 \
   -q -r96 -dSAFER -dBATCH -dNOPAUSE \
   ./temp_logo.eps \
   | convert png:- ./psam_001.gif
') returns nonzero (32512)

Thanks for the quick response!

Harmen

As a followup, the REDUCE Suite has been updated to v2.2.4-2017nov16. The LogoGenerator bug for PDF output has been fixed. The obsolete GIF output has been removed to avoid a dependency on the convert program from ImageMagick. The default PNG format is the choice for use with HTMLSummary-generated webpage. The LogoGenerator documentation has been also revised.

Some examples:


The LogoGenerator utility in the REDUCE Suite is a general purpose, robust logo generator of DNA or RNA base sequences. It creates a logo in the vector EPS format, which can be easily converted to other vector or raster image format using numerous third-party tools. Internally, LogoGenerator takes advantage of the widely available gs program (Ghostscript).

It is worth noting that on Mac OS X, the preview program can directly read LogoGenerator-created EPS file and convert it to PDF format. On Linux and Windows, the situation should be similar.

Xiang-Jun

I can't directly read LogoGenerator-created EPS file on Linux. Am I missing something?

Could you be more specific? Please provide a concrete example so I (and others) can reproduce what you failed to achieve.

Best regards,

Xiang-Jun