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ogotoh / spaln

Genome mapping and spliced alignment of cDNA or amino acid sequences
GNU General Public License v2.0
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Increase MAXL from 256 to _POSIX2_LINE_MAX (2056) #2

Closed nathanweeks closed 4 months ago

nathanweeks commented 6 years ago

While trying to create a bioconda recipe for spaln, I ran into an issue concerning long pathnames generated during the conda build process that cause an error during make install:

make install
...
./makmdm /tmp/miniconda/conda-bld/spaln_1514737890207/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/table

  7.6862  5.1057  4.2546  5.1269  2.0279  4.1061  6.1820  7.4714  2.2983  5.2569
  9.1111  5.9498  2.3414  4.0530  5.0532  6.8225  5.8518  1.4336  3.2303  6.6374
make: *** [install] Abort trap:

This appears to be due to the long pathname exceeding the hard-coded limit in spaln of 256. Bumping up MAXL (which appears to be used for maximum line lengths in files as well) to the POSIX standard _POSIX2_LINE_MAX (defined in limits.h as 2056) resolved the issue.

pvanheus commented 5 years ago

Oh my goodness, I encountered exactly the same issue and made a very similar patch (see the recipe).

pvanheus commented 5 years ago

The issue raised in this PR was addressed in changes committed in spaln version 2.3.3, so this can be closed.