Update to seqan 1.4.2 #105
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* Update aligning with bowtie2 .travis.yml and Makefile. * Add osx case, gccN cases.
This is a backport from bowtie2
commit: c619b9ab47ea1da67bee7258353d0791120384f4 .
This causes an error with gcc 10 & aarch64, s390x, ppc64le.
alphabet.cpp:293:1: error: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ inside { } [-Wnarrowing]
Running the tests with number of threads: 1 on s390x to pass the tests.
SeqAn 1.3 renamed seqan::fill() to seqan::resize().
SeqAn has a class with the same name and fatal name collision happens.
New version 1.4 of SeQan uses a different name of the class
Required by newer versions of GCC.
@mr-c do you have any idea for that? Could you invite the maintainer of bowtie here? |
|
Perhaps, it might be better to manage using https://github.com/seqan/seqan/tree/seqan-v1.4.2 as this repository's git submodule rather than using seqan-library-1.4.2.tar.bz2 . It 's like bowtie2 simde. |
|
I would close this PR, as it seems seqan dependency was dropped by the commit: 3945d8c on Bowtie 1.3.0. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR is working in progress.
Right now bowtie is using seqan 1.1.
And the seqan 1.X's latest version is 1.4.2 according to the downloading side (GitHub).
And actually in both Debian and Fedora, we need to build bowtie with the system seqan deb or RPM package (both package's versions are 1.4.2) patching the some files.
I would like to suggest to use seqan 1.4.2 for this repository.
Let me explain some commits for this PR.
First 3 commits are for the preparation.
1st commit is same with #102 . I expect the PR is merged at first to verify the bowtie.
2nd commit is a backport from bowtie2, that is related to #95 (comment) . Maybe this issue appears running bowtie with gcc-N high version and non-x86_64 architecture.
3rd commit is to run simple-test on s390x. simple-test works with the number of thread: 1 on s390x.
From 4th commit, I used Deiban's patch files. Thank you, Debian people for that.
seqan-library-1.4.2 directory is created like this steps.
Right now there is one CPU architecture common error like this.
See https://travis-ci.org/junaruga/bowtie/jobs/656448871#L1388
Maintainers or Debian people, do you have any idea to fix this?
How do you think to update seqan ?
Thank you.