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update vrna header for SHAPE #120

Merged
merged 4 commits into from
Jun 27, 2018
Merged

update vrna header for SHAPE #120

merged 4 commits into from
Jun 27, 2018

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mmiladi
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@mmiladi mmiladi commented Jun 25, 2018

Vienna RNA headers directory structure has changed in version 2.4.8. This small PR fixes compilation error of linking new vrna-lib with IntaRNA.

@mmiladi
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mmiladi commented Jun 25, 2018

Example of vrna header relocations:
ViennaRNA/ViennaRNA@ebb6675#diff-ab6089775642214db13059c6cd06e423

@RaumZeit
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@mmiladi @martin-mann
It seems you never included <ViennaRNA/constraints-SHAPE.h> directly before but instead implicitly pulled the entire constraints headers through <ViennaRNA/fold_compound.h> or something similar.
Unfortunately, with version 2.4.8 of the ViennaRNA Package we unintentionally broke backward compatibility, where including <ViennaRNA/fold_compound.h> now only pulls the headers for hard and soft constraints...

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mmiladi commented Jun 26, 2018

Thanks much for the tips @RaumZeit .

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Hi @mmiladi
please increase the minimal vrna version (configure.ac) to 2.4.8, to ensure the newly requested header is present!
thanks,
Martin

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@mmiladi just did myself (have seen that I had the rights to.. thanks!)

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vrna 2.4.8 not in bioconda yet...

@martin-raden martin-raden merged commit 412be51 into BackofenLab:master Jun 27, 2018
martin-raden added a commit that referenced this pull request Jun 27, 2018
@martin-raden
Revert "update vrna header for SHAPE (#120)"
614e8c4 
This reverts commit 412be51.
martin-raden added a commit that referenced this pull request Jun 27, 2018
@martin-raden
update vrna header for SHAPE (#120) (#121)
6ab4972 
* update vrna header for SHAPE

* bump VRNA_REQUIRED_VERSION to 2.4.8

* vienna min version updated

* minimal vienna version bumped to 2.4.8
martin-raden added a commit that referenced this pull request Jun 27, 2018
@martin-raden
adaptation to vrna 2.4.8 (#122)
5cbf5c2 
* * multi-threading output issues tackled

* version 2.2.0

* "version" outputs VRNA and boost version

* github release link description changed

from "Github" to "releases"

* update vrna header for SHAPE (#120) (#121)

* update vrna header for SHAPE

* bump VRNA_REQUIRED_VERSION to 2.4.8

* vienna min version updated

* minimal vienna version bumped to 2.4.8

* adaption documented
martin-raden added a commit that referenced this pull request Sep 5, 2018
@martin-raden
update dev-branch (#126)
86088a2 
* adaptation to vrna 2.4.8 (#122)

* * multi-threading output issues tackled

* version 2.2.0

* "version" outputs VRNA and boost version

* github release link description changed

from "Github" to "releases"

* update vrna header for SHAPE (#120) (#121)

* update vrna header for SHAPE

* bump VRNA_REQUIRED_VERSION to 2.4.8

* vienna min version updated

* minimal vienna version bumped to 2.4.8

* adaption documented

* version 2.2.1

* version 2.2.1

* update travis build (pkg-config)
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3 participants
@mmiladi @RaumZeit @martin-raden