[Bioc-devel] Problems caused by earlier Rhtslib migration

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Wed Apr 1 18:03:30 CEST 2020

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 

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.


> Best regards,
> Antti
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uZWZ6Z8-kMo46tPlCV-srVxHQ6g2EjpgilOYFeyGxYw&s=LuTyhFobrvTJ5otx3h60JgLILxjQvqeXR4XC9xHdHEI&e= 

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list