GNU bug report logs - #28384
[PATCH] gnu: Fix build failures caused by commit.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Kei Kebreau <kkebreau <at> posteo.net>
Subject: [PATCH] gnu: Fix build failures caused by commit.
Date: Thu,  7 Sep 2017 12:43:40 -0400

* gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
* gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
---
 gnu/packages/bioinformatics.scm | 2 ++
 gnu/packages/ci.scm             | 6 +++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bf8eb2e69..699c463bf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4488,6 +4488,8 @@ distribution, coverage uniformity, strand specificity, etc.")
            (modify-phases %standard-phases
              (add-after 'unpack 'bootstrap
                (lambda _
+                 (substitute* "gen_tools_am"
+                   (("/usr/bin/env perl") (which "perl")))
                  (zero? (system* "bash" "gen_auto"))))
              (add-after 'build 'build-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index c449754be..3b182b826 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -216,7 +216,11 @@ their dependencies.")
                (substitute* "Makefile.am"
                  (("tests/repo.scm \\\\") "\\"))
                #t))
-           (add-after 'disable-repo-tests 'bootstrap
+           (add-after 'disable-repo-tests 'patch-/bin/sh
+             (lambda _
+               (substitute* "build-aux/git-version-gen"
+                 (("#!/bin/sh") (string-append "#!" (which "sh"))))))
+           (add-after 'patch-/bin/sh 'bootstrap
              (lambda _ (zero? (system* "sh" "bootstrap"))))
            (add-after 'install 'wrap-program
              (lambda* (#:key inputs outputs #:allow-other-keys)
-- 
2.14.1

Message #8 received at 28384 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Kei Kebreau <kkebreau <at> posteo.net>
Cc: 28384 <at> debbugs.gnu.org
Subject: Re: [bug#28384] [PATCH] gnu: Fix build failures caused by commit.
Date: Fri, 08 Sep 2017 17:43:13 +0200

Hi Kei,

The subject is truncated.  :-)  Caused by which commit?

Kei Kebreau <kkebreau <at> posteo.net> skribis:

> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.

This is weird, normally the ‘patch-source-shebangs’ phase, which happens
right before ‘configure’, should take care of these, no?

> diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
> index c449754be..3b182b826 100644
> --- a/gnu/packages/ci.scm
> +++ b/gnu/packages/ci.scm
> @@ -216,7 +216,11 @@ their dependencies.")
>                 (substitute* "Makefile.am"
>                   (("tests/repo.scm \\\\") "\\"))
>                 #t))
> -           (add-after 'disable-repo-tests 'bootstrap
> +           (add-after 'disable-repo-tests 'patch-/bin/sh
> +             (lambda _
> +               (substitute* "build-aux/git-version-gen"
> +                 (("#!/bin/sh") (string-append "#!" (which "sh"))))))

This phase should return #t.

Thanks,
Ludo’.

Message #11 received at 28384 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: ludo <at> gnu.org (Ludovic Courtès)
Cc: 28384 <at> debbugs.gnu.org
Subject: Re: [bug#28384] [PATCH] gnu: Fix build failures caused by commit.
Date: Fri, 08 Sep 2017 12:41:49 -0400

[Message part 1 (text/plain, inline)]

ludo <at> gnu.org (Ludovic Courtès) writes:

> Hi Kei,
>
> The subject is truncated.  :-)  Caused by which commit?
>
> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>
>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>
> This is weird, normally the ‘patch-source-shebangs’ phase, which happens
> right before ‘configure’, should take care of these, no?
>

Normally the 'patch-source-shebangs' does just that, but in this case
the script needs to be patched because the bootstrapping phase depends
on perl.

>> diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
>> index c449754be..3b182b826 100644
>> --- a/gnu/packages/ci.scm
>> +++ b/gnu/packages/ci.scm
>> @@ -216,7 +216,11 @@ their dependencies.")
>>                 (substitute* "Makefile.am"
>>                   (("tests/repo.scm \\\\") "\\"))
>>                 #t))
>> -           (add-after 'disable-repo-tests 'bootstrap
>> +           (add-after 'disable-repo-tests 'patch-/bin/sh
>> +             (lambda _
>> +               (substitute* "build-aux/git-version-gen"
>> +                 (("#!/bin/sh") (string-append "#!" (which "sh"))))))
>
> This phase should return #t.

Thanks for catching that.

>
> Thanks,
> Ludo’.

[0001-gnu-Use-modify-phases-syntax.patch (text/plain, attachment)]

[signature.asc (application/pgp-signature, inline)]

Message #14 received at 28384 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Kei Kebreau <kkebreau <at> posteo.net>
Cc: 28384 <at> debbugs.gnu.org
Subject: Re: [bug#28384] [PATCH] gnu: Fix build failures caused by commit.
Date: Fri, 08 Sep 2017 22:33:27 +0200

Kei Kebreau <kkebreau <at> posteo.net> skribis:

> ludo <at> gnu.org (Ludovic Courtès) writes:
>
>> Hi Kei,
>>
>> The subject is truncated.  :-)  Caused by which commit?
>>
>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>
>>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>>
>> This is weird, normally the ‘patch-source-shebangs’ phase, which happens
>> right before ‘configure’, should take care of these, no?
>>
>
> Normally the 'patch-source-shebangs' does just that, but in this case
> the script needs to be patched because the bootstrapping phase depends
> on perl.

OK.  I don’t understand at what point this became necessary though.

> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
> From: Kei Kebreau <kkebreau <at> posteo.net>
> Date: Sat, 29 Jul 2017 11:28:42 -0400
> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
> To: guix-patches <at> gnu.org

Wrong patch.  :-)

Ludo’.

Message #17 received at 28384 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: ludo <at> gnu.org (Ludovic Courtès)
Cc: 28384 <at> debbugs.gnu.org
Subject: Re: [bug#28384] [PATCH] gnu: Fix build failures caused by commit.
Date: Fri, 08 Sep 2017 18:10:14 -0400

[Message part 1 (text/plain, inline)]

ludo <at> gnu.org (Ludovic Courtès) writes:

> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>
>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>
>>> Hi Kei,
>>>
>>> The subject is truncated.  :-)  Caused by which commit?
>>>
>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>
>>>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>>>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>>>
>>> This is weird, normally the ‘patch-source-shebangs’ phase, which happens
>>> right before ‘configure’, should take care of these, no?
>>>
>>
>> Normally the 'patch-source-shebangs' does just that, but in this case
>> the script needs to be patched because the bootstrapping phase depends
>> on perl.
>
> OK.  I don’t understand at what point this became necessary though.
>

It's probably a result of moving the 'bootstrap' phase before the
'patch-source-shebangs' phase. Without this change, the seek package
builds fine. I have no preference either way, though I notice that the
same thing is done for guile-for-guile-emacs.

>> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
>> From: Kei Kebreau <kkebreau <at> posteo.net>
>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>> To: guix-patches <at> gnu.org
>
> Wrong patch.  :-)
>
> Ludo’.

Fixed!

[0001-gnu-Fix-build-failures-caused-by-commit.patch (text/plain, attachment)]

[signature.asc (application/pgp-signature, inline)]

Message #20 received at 28384 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Kei Kebreau <kkebreau <at> posteo.net>
Cc: 28384 <at> debbugs.gnu.org
Subject: Re: [bug#28384] [PATCH] gnu: Fix build failures caused by commit.
Date: Sun, 10 Sep 2017 14:53:32 +0200

Kei Kebreau <kkebreau <at> posteo.net> skribis:

> ludo <at> gnu.org (Ludovic Courtès) writes:
>
>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>
>>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>>
>>>> Hi Kei,
>>>>
>>>> The subject is truncated.  :-)  Caused by which commit?
>>>>
>>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>>
>>>>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>>>>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>>>>
>>>> This is weird, normally the ‘patch-source-shebangs’ phase, which happens
>>>> right before ‘configure’, should take care of these, no?
>>>>
>>>
>>> Normally the 'patch-source-shebangs' does just that, but in this case
>>> the script needs to be patched because the bootstrapping phase depends
>>> on perl.
>>
>> OK.  I don’t understand at what point this became necessary though.
>>
>
> It's probably a result of moving the 'bootstrap' phase before the
> 'patch-source-shebangs' phase. Without this change, the seek package
> builds fine. I have no preference either way, though I notice that the
> same thing is done for guile-for-guile-emacs.

Since this commit was just about changing the syntax, not the semantics,
I would expect it to keep phases in the same order.  That would be more
concise than adding custom code to patch things here and there, no?

WDYT?

>>> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
>>> From: Kei Kebreau <kkebreau <at> posteo.net>
>>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>>> To: guix-patches <at> gnu.org
>>
>> Wrong patch.  :-)
>>
>> Ludo’.
>
> Fixed!
>
> From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
> From: Kei Kebreau <kkebreau <at> posteo.net>
> Date: Thu, 7 Sep 2017 09:36:28 -0400
> Subject: [PATCH] gnu: Fix build failures caused by commit
>  d10092b849153dc27cfed0a9601fde6c7bdec918.
>
> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.

That’s fine with me, even though I have a slight preference for simply
restoring the order of phases as it was before.

Thanks!

Ludo’.

Message #23 received at 28384 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: ludo <at> gnu.org (Ludovic Courtès)
Cc: 28384 <at> debbugs.gnu.org
Subject: Re: [bug#28384] [PATCH] gnu: Fix build failures caused by commit.
Date: Sun, 10 Sep 2017 09:32:23 -0400

[Message part 1 (text/plain, inline)]

ludo <at> gnu.org (Ludovic Courtès) writes:

> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>
>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>
>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>
>>>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>>>
>>>>> Hi Kei,
>>>>>
>>>>> The subject is truncated.  :-)  Caused by which commit?
>>>>>
>>>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>>>
>>>>>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>>>>>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>>>>>
>>>>> This is weird, normally the ‘patch-source-shebangs’ phase, which happens
>>>>> right before ‘configure’, should take care of these, no?
>>>>>
>>>>
>>>> Normally the 'patch-source-shebangs' does just that, but in this case
>>>> the script needs to be patched because the bootstrapping phase depends
>>>> on perl.
>>>
>>> OK.  I don’t understand at what point this became necessary though.
>>>
>>
>> It's probably a result of moving the 'bootstrap' phase before the
>> 'patch-source-shebangs' phase. Without this change, the seek package
>> builds fine. I have no preference either way, though I notice that the
>> same thing is done for guile-for-guile-emacs.
>
> Since this commit was just about changing the syntax, not the semantics,
> I would expect it to keep phases in the same order.  That would be more
> concise than adding custom code to patch things here and there, no?
>
> WDYT?
>

I agree in the case of seek.

>>>> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
>>>> From: Kei Kebreau <kkebreau <at> posteo.net>
>>>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>>>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>>>> To: guix-patches <at> gnu.org
>>>
>>> Wrong patch.  :-)
>>>
>>> Ludo’.
>>
>> Fixed!
>>
>> From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
>> From: Kei Kebreau <kkebreau <at> posteo.net>
>> Date: Thu, 7 Sep 2017 09:36:28 -0400
>> Subject: [PATCH] gnu: Fix build failures caused by commit
>>  d10092b849153dc27cfed0a9601fde6c7bdec918.
>>
>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>
> That’s fine with me, even though I have a slight preference for simply
> restoring the order of phases as it was before.
>

I'm most comfortable reverting seek to its last successful state without
the substitute* call and patch leave the cuirass patch as is. If that's
okay with you I can push this to master.

> Thanks!
>
> Ludo’.

Thanks for helping to sort this out!

[signature.asc (application/pgp-signature, inline)]

Message #26 received at 28384 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Kei Kebreau <kkebreau <at> posteo.net>
Cc: 28384 <at> debbugs.gnu.org
Subject: Re: [bug#28384] [PATCH] gnu: Fix build failures caused by commit.
Date: Sun, 10 Sep 2017 22:39:28 +0200

Kei Kebreau <kkebreau <at> posteo.net> skribis:

> ludo <at> gnu.org (Ludovic Courtès) writes:
>
>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>
>>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>>
>>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>>
>>>>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>>>>
>>>>>> Hi Kei,
>>>>>>
>>>>>> The subject is truncated.  :-)  Caused by which commit?
>>>>>>
>>>>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>>>>
>>>>>>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>>>>>>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>>>>>>
>>>>>> This is weird, normally the ‘patch-source-shebangs’ phase, which happens
>>>>>> right before ‘configure’, should take care of these, no?
>>>>>>
>>>>>
>>>>> Normally the 'patch-source-shebangs' does just that, but in this case
>>>>> the script needs to be patched because the bootstrapping phase depends
>>>>> on perl.
>>>>
>>>> OK.  I don’t understand at what point this became necessary though.
>>>>
>>>
>>> It's probably a result of moving the 'bootstrap' phase before the
>>> 'patch-source-shebangs' phase. Without this change, the seek package
>>> builds fine. I have no preference either way, though I notice that the
>>> same thing is done for guile-for-guile-emacs.
>>
>> Since this commit was just about changing the syntax, not the semantics,
>> I would expect it to keep phases in the same order.  That would be more
>> concise than adding custom code to patch things here and there, no?
>>
>> WDYT?
>>
>
> I agree in the case of seek.
>
>>>>> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
>>>>> From: Kei Kebreau <kkebreau <at> posteo.net>
>>>>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>>>>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>>>>> To: guix-patches <at> gnu.org
>>>>
>>>> Wrong patch.  :-)
>>>>
>>>> Ludo’.
>>>
>>> Fixed!
>>>
>>> From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
>>> From: Kei Kebreau <kkebreau <at> posteo.net>
>>> Date: Thu, 7 Sep 2017 09:36:28 -0400
>>> Subject: [PATCH] gnu: Fix build failures caused by commit
>>>  d10092b849153dc27cfed0a9601fde6c7bdec918.
>>>
>>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>>
>> That’s fine with me, even though I have a slight preference for simply
>> restoring the order of phases as it was before.
>>
>
> I'm most comfortable reverting seek to its last successful state without
> the substitute* call and patch leave the cuirass patch as is. If that's
> okay with you I can push this to master.

Sounds good, thanks!

Ludo'.

Message #31 received at 28384-done <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: ludo <at> gnu.org (Ludovic Courtès)
Cc: 28384-done <at> debbugs.gnu.org
Subject: Re: [bug#28384] [PATCH] gnu: Fix build failures caused by commit.
Date: Sun, 10 Sep 2017 18:26:39 -0400

ludo <at> gnu.org (Ludovic Courtès) writes:

> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>
>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>
>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>
>>>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>>>
>>>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>>>
>>>>>> ludo <at> gnu.org (Ludovic Courtès) writes:
>>>>>>
>>>>>>> Hi Kei,
>>>>>>>
>>>>>>> The subject is truncated.  :-)  Caused by which commit?
>>>>>>>
>>>>>>> Kei Kebreau <kkebreau <at> posteo.net> skribis:
>>>>>>>
>>>>>>>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify
>>>>>>>> unpack phase.
>>>>>>>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>>>>>>>
>>>>>>> This is weird, normally the ‘patch-source-shebangs’ phase, which happens
>>>>>>> right before ‘configure’, should take care of these, no?
>>>>>>>
>>>>>>
>>>>>> Normally the 'patch-source-shebangs' does just that, but in this case
>>>>>> the script needs to be patched because the bootstrapping phase depends
>>>>>> on perl.
>>>>>
>>>>> OK.  I don’t understand at what point this became necessary though.
>>>>>
>>>>
>>>> It's probably a result of moving the 'bootstrap' phase before the
>>>> 'patch-source-shebangs' phase. Without this change, the seek package
>>>> builds fine. I have no preference either way, though I notice that the
>>>> same thing is done for guile-for-guile-emacs.
>>>
>>> Since this commit was just about changing the syntax, not the semantics,
>>> I would expect it to keep phases in the same order.  That would be more
>>> concise than adding custom code to patch things here and there, no?
>>>
>>> WDYT?
>>>
>>
>> I agree in the case of seek.
>>
>>>>>> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
>>>>>> From: Kei Kebreau <kkebreau <at> posteo.net>
>>>>>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>>>>>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>>>>>> To: guix-patches <at> gnu.org
>>>>>
>>>>> Wrong patch.  :-)
>>>>>
>>>>> Ludo’.
>>>>
>>>> Fixed!
>>>>
>>>> From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
>>>> From: Kei Kebreau <kkebreau <at> posteo.net>
>>>> Date: Thu, 7 Sep 2017 09:36:28 -0400
>>>> Subject: [PATCH] gnu: Fix build failures caused by commit
>>>>  d10092b849153dc27cfed0a9601fde6c7bdec918.
>>>>
>>>> * gnu/packages/bioinformatics.scm (seek)[arguments]: Modify unpack phase.
>>>> * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
>>>
>>> That’s fine with me, even though I have a slight preference for simply
>>> restoring the order of phases as it was before.
>>>
>>
>> I'm most comfortable reverting seek to its last successful state without
>> the substitute* call and patch leave the cuirass patch as is. If that's
>> okay with you I can push this to master.
>
> Sounds good, thanks!
>
> Ludo'.

Pushed to master as 4561498e1f207e83ecc4a9fe1a08935c2807160f. Thanks again!

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