Elementolab/ChIPseeqer2.0 known issues

Known issues for ChIPseeqer-2.0

These errors will be fixed in the next release.

In the meantime, here's how you can address them.

1. kohonen.c fails to compile (on Mac OS X)

when:

make tools

what:

kohonen.c:17:20: error: values.h: No such file or directory
make[1]: *** [kohonen] Error 1

how to address:

a. Go to ChIPseeqer-2.0/tools/KOHONEN
b. open kohonen.c with a text editor
c. remove line 17: include <values.h>
OR replace kohonen.c with this

2. Segmentation fault in ChIPseeqerMakeGeneEnrichmentData

when: when running ChIPseeqerPlotAverageReadDensityInGenes

what: sh: line 1: 17508 Segmentation fault

how to address:

a. Go to ChIPseeqer-2.0/dist
b. open ChIPseeqerPlotAverageReadDensityInGenes with a text editor
c. edit line 121

from

$annotation            = "$ENV{CHIPSEEQERDIR}/DATA/$genome/$db.new";

$annotation            = "$ENV{CHIPSEEQERDIR}/DATA/$genome/$db";

3. Macports (Mac OS X)

Packages installation with Macports