Hi Antti,
On 3/30/20 00:14, Antti Honkela wrote:
Hi all,
I am a co-maintainer of BitSeq. About a year ago, we were offered help
in migration from Rsamtools to Rhtslib and we took the offer.
The commit pushed by BioC team added a file src/bam_plbuf.c with just
one line:
#include <bam_plbuf.c>
This is now making our Windows build fail because of an infinite include
loop.
As I don't understand why the file was added in the first place, help in
resolving the issue would be appreciated!
This is a trick to put a copy of the bam_plbuf.c file from the Rhtslib
package in BitSeq/src/. I used the same trick for 7 other packages that
I also migrated from Rsamtools to Rhtslib and it works fine on all
platforms, including Windows. Not sure what's special about BitSeq on
Windows.
Can you please try to rename the file e.g. to Rhtslib_bam_plbuf.c? This
should avoid the "include nested too deeply" error, hopefully. You might
want to do the same thing for the sam.c file.
Thanks,
H.
Best regards,
Antti
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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