flexbar
flexbar copied to clipboard
seqan
Please upgrade to onetbb
Hi, Debian has migrated to onetbb (the successor of tbb). Unfortunately flexbar does not build with the new API as you can read in the bug report against the Debian package which says:
/<<PKGBUILDDIR>>/src/Flexbar.h:15:10: fatal error: tbb/pipeline.h: No such file or directory
15 | #include <tbb/pipeline.h>
| ^~~~~~~~~~~~~~~~
compilation terminated.
It would be great if flexbar would support this new API. Kind regards, Andreas.
Any news about this? Please note that flexbar can not be distributed with the next stable release if this will not be fixed.
Hi, Andreas.
I've just cloned the "flexbar" GitHub repo and compiled it successfully from source under Ubuntu-MATE 22.04 LTS + med-bio + med=bio-dev
I'm not sure what the precise relationship between Debian and Ubuntu is, but there are no "onetbb" packages available for Ubuntu 2022.04 LTS
Bye,
Tony.
Am Sun, Dec 18, 2022 at 03:11:48PM -0800 schrieb Tony Travis:
I'm not sure what the precise relationship between Debian and Ubuntu is, but there are no "onetbb" packages available for Ubuntu 2022.04 LTS
As per bug report the soon to be released Debian is affected and thus future Ubuntu versions. Andreas.
I just like to repeat: If you want to have flexbar in the next Debian stable release as well as future Ubuntu releases it is time to act upon this issue now.
The email address of the first author [email protected] no longer exists and I have not had a reply from my email to [email protected], who was a also an email contact on the https://pubmed.ncbi.nlm.nih.gov/28541403/ paper. Sadly, I think Flexbar should now be considered 'orphanware' because of no response from upstream either here of by email.
@tillea I've made an initial attempt at this in #41 if helpful for you
I don't actually use this software directly so haven't been able to test it, but at least it compiles...
Hi,
Am Thu, Feb 09, 2023 at 07:56:16AM -0800 schrieb Liam Keegan:
@tillea I've made an initial attempt at this in #41 if helpful for you
I don't actually use this software directly so haven't been able to test it, but at least it compiles...
Thanks a lot for the patch. I confirm the binary builds with your patch which I applied to the Debian packaging. Unfortunately the test seems to end in some endless loop:
cd test ; \
export PATH="/build/flexbar-3.5.0/obj-x86_64-linux-gnu:$PATH" ; \
echo $PATH ; \
export HOME=/tmp ; \
which flexbar ; \
./flexbar_test.sh
/build/flexbar-3.5.0/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin
/build/flexbar-3.5.0/obj-x86_64-linux-gnu/flexbar
Testing fasta:
Hopefully someone will be able to fire up gdb and find a fix.
Kind regards, Andreas.