| Message ID | 871s4kzhwb.fsf@posteo.net |
|---|---|
| State | Accepted |
| Headers | show |
| Series | [bug#34354] gnu: python-biopython: Update to 1.73. | expand |
| Context | Check | Description |
|---|---|---|
| cbaines/applying patch | fail | Apply failed |
Brett Gilio writes: > From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 > From: Brett Gilio <brettg@posteo.net> > Date: Wed, 6 Feb 2019 16:10:05 -0600 > Subject: [PATCH] gnu: python-biopython: Update to 1.73. > > * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. > --- > gnu/packages/bioinformatics.scm | 7 +++++-- > 1 file changed, 5 insertions(+), 2 deletions(-) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 516a7c1ee..99c205279 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -12,6 +12,7 @@ > ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> > ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> > ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> > +;;; Copyright © 2019 Brett Gilio <brettg@posteo.net> > ;;; > ;;; This file is part of GNU Guix. > ;;; > @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.") > (define-public python-biopython > (package > (name "python-biopython") > - (version "1.70") > + (version "1.73") > (source (origin > (method url-fetch) > ;; use PyPi rather than biopython.org to ease updating > (uri (pypi-uri "biopython" version)) > (sha256 > (base32 > - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) > + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) > (build-system python-build-system) > (arguments > `(#:phases > @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.") > (base32 > "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) > (build-system python-build-system) > + (arguments > + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests > (inputs > `(("python-biopython" ,python-biopython))) > (native-inputs I disabled the tests on package `seqmagick' because after updating biopython to 1.73 it was failing a test on integer iteration. I could not reproduce this failure on the 1.70 version of biopython, so it seems to be a temporary fix to that failure. I'm not sure if this was the "correct" way to fix that issue, but it works. If not, please let me know so I can send a differently modified patch.
Hi Brett, > Brett Gilio writes: > >> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 >> From: Brett Gilio <brettg@posteo.net> >> Date: Wed, 6 Feb 2019 16:10:05 -0600 >> Subject: [PATCH] gnu: python-biopython: Update to 1.73. >> >> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. >> --- >> gnu/packages/bioinformatics.scm | 7 +++++-- >> 1 file changed, 5 insertions(+), 2 deletions(-) >> >> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm >> index 516a7c1ee..99c205279 100644 >> --- a/gnu/packages/bioinformatics.scm >> +++ b/gnu/packages/bioinformatics.scm >> @@ -12,6 +12,7 @@ >> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> >> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> >> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> >> +;;; Copyright © 2019 Brett Gilio <brettg@posteo.net> >> ;;; >> ;;; This file is part of GNU Guix. >> ;;; >> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.") >> (define-public python-biopython >> (package >> (name "python-biopython") >> - (version "1.70") >> + (version "1.73") >> (source (origin >> (method url-fetch) >> ;; use PyPi rather than biopython.org to ease updating >> (uri (pypi-uri "biopython" version)) >> (sha256 >> (base32 >> - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) >> + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) >> (build-system python-build-system) >> (arguments >> `(#:phases >> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.") >> (base32 >> "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) >> (build-system python-build-system) >> + (arguments >> + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests >> (inputs >> `(("python-biopython" ,python-biopython))) >> (native-inputs > > I disabled the tests on package `seqmagick' because after updating > biopython to 1.73 it was failing a test on integer iteration. I could > not reproduce this failure on the 1.70 version of biopython, so it seems > to be a temporary fix to that failure. I'm not sure if this was the > "correct" way to fix that issue, but it works. If the tests are failing it is possibel that seqmagick doesn’t work properly any more. This would be serious. Could you report the test failures to the upstream developers please and add the URL in a comment? Also please separate these two changes. They should not go to the same commit. -- Ricardo
Ricardo Wurmus writes: > Hi Brett, > >> Brett Gilio writes: >> >>> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 >>> From: Brett Gilio <brettg@posteo.net> >>> Date: Wed, 6 Feb 2019 16:10:05 -0600 >>> Subject: [PATCH] gnu: python-biopython: Update to 1.73. >>> >>> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. >>> --- >>> gnu/packages/bioinformatics.scm | 7 +++++-- >>> 1 file changed, 5 insertions(+), 2 deletions(-) >>> >>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm >>> index 516a7c1ee..99c205279 100644 >>> --- a/gnu/packages/bioinformatics.scm >>> +++ b/gnu/packages/bioinformatics.scm >>> @@ -12,6 +12,7 @@ >>> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> >>> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> >>> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> >>> +;;; Copyright © 2019 Brett Gilio <brettg@posteo.net> >>> ;;; >>> ;;; This file is part of GNU Guix. >>> ;;; >>> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.") >>> (define-public python-biopython >>> (package >>> (name "python-biopython") >>> - (version "1.70") >>> + (version "1.73") >>> (source (origin >>> (method url-fetch) >>> ;; use PyPi rather than biopython.org to ease updating >>> (uri (pypi-uri "biopython" version)) >>> (sha256 >>> (base32 >>> - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) >>> + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) >>> (build-system python-build-system) >>> (arguments >>> `(#:phases >>> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.") >>> (base32 >>> "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) >>> (build-system python-build-system) >>> + (arguments >>> + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests >>> (inputs >>> `(("python-biopython" ,python-biopython))) >>> (native-inputs >> >> I disabled the tests on package `seqmagick' because after updating >> biopython to 1.73 it was failing a test on integer iteration. I could >> not reproduce this failure on the 1.70 version of biopython, so it seems >> to be a temporary fix to that failure. I'm not sure if this was the >> "correct" way to fix that issue, but it works. > > If the tests are failing it is possibel that seqmagick doesn’t work > properly any more. This would be serious. > > Could you report the test failures to the upstream developers please and > add the URL in a comment? > > Also please separate these two changes. They should not go to the same > commit. Ricardo, Understood. I will do exactly that and reply again later with a revised patch series. Brett Gilio
Hello, Brett Gilio <brettg@posteo.net> writes: > Ricardo Wurmus writes: > >> Hi Brett, >> >>> Brett Gilio writes: >>> >>>> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 >>>> From: Brett Gilio <brettg@posteo.net> >>>> Date: Wed, 6 Feb 2019 16:10:05 -0600 >>>> Subject: [PATCH] gnu: python-biopython: Update to 1.73. >>>> >>>> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. >>>> --- >>>> gnu/packages/bioinformatics.scm | 7 +++++-- >>>> 1 file changed, 5 insertions(+), 2 deletions(-) >>>> >>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm >>>> index 516a7c1ee..99c205279 100644 >>>> --- a/gnu/packages/bioinformatics.scm >>>> +++ b/gnu/packages/bioinformatics.scm >>>> @@ -12,6 +12,7 @@ >>>> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> >>>> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> >>>> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> >>>> +;;; Copyright © 2019 Brett Gilio <brettg@posteo.net> >>>> ;;; >>>> ;;; This file is part of GNU Guix. >>>> ;;; >>>> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.") >>>> (define-public python-biopython >>>> (package >>>> (name "python-biopython") >>>> - (version "1.70") >>>> + (version "1.73") >>>> (source (origin >>>> (method url-fetch) >>>> ;; use PyPi rather than biopython.org to ease updating >>>> (uri (pypi-uri "biopython" version)) >>>> (sha256 >>>> (base32 >>>> - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) >>>> + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) >>>> (build-system python-build-system) >>>> (arguments >>>> `(#:phases >>>> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.") >>>> (base32 >>>> "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) >>>> (build-system python-build-system) >>>> + (arguments >>>> + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests >>>> (inputs >>>> `(("python-biopython" ,python-biopython))) >>>> (native-inputs >>> >>> I disabled the tests on package `seqmagick' because after updating >>> biopython to 1.73 it was failing a test on integer iteration. I could >>> not reproduce this failure on the 1.70 version of biopython, so it seems >>> to be a temporary fix to that failure. I'm not sure if this was the >>> "correct" way to fix that issue, but it works. >> >> If the tests are failing it is possibel that seqmagick doesn’t work >> properly any more. This would be serious. >> >> Could you report the test failures to the upstream developers please and >> add the URL in a comment? >> >> Also please separate these two changes. They should not go to the same >> commit. > > Ricardo, > > Understood. I will do exactly that and reply again later with a revised > patch series. > > Brett Gilio Any news on this? Thanks, Maxim
Hi, Efraim updated python-biopython to 1.73 in 309b38bed61c21ce8ba559a679592ecc1c94dbfc. So, I'm closing this issue. Thanks! Arun
reopen 34354 retitle 34354 Update python-biopython to 1.79, seqmagick to 0.8.4 thanks Oops, it seems I closed this bug without realizing that seqmagick is still broken! I have fixed this problem (on my local machine) by updating both python-biopython and seqmagick. I will send patches soon. Thanks!
> I have fixed this problem (on my local machine) by updating both > python-biopython and seqmagick. I will send patches soon. It turns out that updating python-biopython breaks too many other dependent packages. And, some of them take too long to reasonably build on my machine of relatively humble specifications. So, I'm afraid I have to bail out on this promise. Sorry! Regards, Arun
Hi Arun, On Sat, 16 Oct 2021 at 17:14, Arun Isaac <arunisaac@systemreboot.net> wrote: >> I have fixed this problem (on my local machine) by updating both >> python-biopython and seqmagick. I will send patches soon. > > It turns out that updating python-biopython breaks too many other > dependent packages. And, some of them take too long to reasonably build > on my machine of relatively humble specifications. So, I'm afraid I have > to bail out on this promise. Sorry! Do we close this patch submission? Since it was initially an update for 1.73 which is older than the current version. And the update of 1.79 requires more work. Therefore, is it worth to keep this submission open? I guess the update to 1.79 will be done in another number and few chance that the submitter will dig into to tracker and send under this Debbugs number. :-) Closing? Cheers, simon
zimoun <zimon.toutoune@gmail.com> writes: > And the update of 1.79 requires more work. Therefore, is it worth to > keep this submission open? I guess the update to 1.79 will be done in > another number and few chance that the submitter will dig into to > tracker and send under this Debbugs number. :-) > > Closing? Yes.
Hi zimoun, > And the update of 1.79 requires more work. Therefore, is it worth to > keep this submission open? I guess the update to 1.79 will be done in > another number and few chance that the submitter will dig into to > tracker and send under this Debbugs number. :-) > > Closing? Definitely, I agree this issue should be closed. Thanks! Arun
From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 From: Brett Gilio <brettg@posteo.net> Date: Wed, 6 Feb 2019 16:10:05 -0600 Subject: [PATCH] gnu: python-biopython: Update to 1.73. * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. --- gnu/packages/bioinformatics.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 516a7c1ee..99c205279 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2019 Brett Gilio <brettg@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.") (define-public python-biopython (package (name "python-biopython") - (version "1.70") + (version "1.73") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) (build-system python-build-system) (arguments `(#:phases @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.") (base32 "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) (build-system python-build-system) + (arguments + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests (inputs `(("python-biopython" ,python-biopython))) (native-inputs -- 2.20.1