[PATCH] gnu: Fix build failures caused by commit.

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2 participants
  • Kei Kebreau
  • Ludovic Courtès
Owner
unassigned
Submitted by
Kei Kebreau
Severity
normal

Debbugs page

Kei Kebreau wrote 8 years ago
(address . guix-patches@gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)
20170907164340.32328-1-kkebreau@posteo.net
* 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(-)

Toggle diff (32 lines)
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
Ludovic Courtès wrote 8 years ago
(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 28384@debbugs.gnu.org)
87o9ql9oxa.fsf@gnu.org
Hi Kei,

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

Kei Kebreau <kkebreau@posteo.net> skribis:

Toggle quote (3 lines)
> * 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?

Toggle quote (14 lines)
> 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’.
Kei Kebreau wrote 8 years ago
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 28384@debbugs.gnu.org)
87377xdtwy.fsf@posteo.net
ludo@gnu.org (Ludovic Courtès) writes:

Toggle quote (13 lines)
> Hi Kei,
>
> The subject is truncated. :-) Caused by which commit?
>
> Kei Kebreau <kkebreau@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.

Toggle quote (16 lines)
>> 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.

Toggle quote (3 lines)
>
> Thanks,
> Ludo’.
Attachment: 0001-gnu-Use-modify-phases-syntax.patch
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Ludovic Courtès wrote 8 years ago
(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 28384@debbugs.gnu.org)
87efrh9bhk.fsf@gnu.org
Kei Kebreau <kkebreau@posteo.net> skribis:

Toggle quote (19 lines)
> ludo@gnu.org (Ludovic Courtès) writes:
>
>> Hi Kei,
>>
>> The subject is truncated. :-) Caused by which commit?
>>
>> Kei Kebreau <kkebreau@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.

Toggle quote (6 lines)
> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
> From: Kei Kebreau <kkebreau@posteo.net>
> Date: Sat, 29 Jul 2017 11:28:42 -0400
> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
> To: guix-patches@gnu.org

Wrong patch. :-)

Ludo’.
Kei Kebreau wrote 8 years ago
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 28384@debbugs.gnu.org)
87y3podepl.fsf@posteo.net
ludo@gnu.org (Ludovic Courtès) writes:

Toggle quote (24 lines)
> Kei Kebreau <kkebreau@posteo.net> skribis:
>
>> ludo@gnu.org (Ludovic Courtès) writes:
>>
>>> Hi Kei,
>>>
>>> The subject is truncated. :-) Caused by which commit?
>>>
>>> Kei Kebreau <kkebreau@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.

Toggle quote (10 lines)
>> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
>> From: Kei Kebreau <kkebreau@posteo.net>
>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>> To: guix-patches@gnu.org
>
> Wrong patch. :-)
>
> Ludo’.

Fixed!
From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@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.
---
gnu/packages/bioinformatics.scm | 2 ++
gnu/packages/ci.scm | 7 ++++++-
2 files changed, 8 insertions(+), 1 deletion(-)

Toggle diff (33 lines)
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..f3259bfcd 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -216,7 +216,12 @@ 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"))))
+ #t))
+ (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
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Ludovic Courtès wrote 8 years ago
(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 28384@debbugs.gnu.org)
87mv6290kz.fsf@gnu.org
Kei Kebreau <kkebreau@posteo.net> skribis:

Toggle quote (31 lines)
> ludo@gnu.org (Ludovic Courtès) writes:
>
>> Kei Kebreau <kkebreau@posteo.net> skribis:
>>
>>> ludo@gnu.org (Ludovic Courtès) writes:
>>>
>>>> Hi Kei,
>>>>
>>>> The subject is truncated. :-) Caused by which commit?
>>>>
>>>> Kei Kebreau <kkebreau@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?

Toggle quote (21 lines)
>>> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
>>> From: Kei Kebreau <kkebreau@posteo.net>
>>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>>> To: guix-patches@gnu.org
>>
>> Wrong patch. :-)
>>
>> Ludo’.
>
> Fixed!
>
> From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
> From: Kei Kebreau <kkebreau@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’.
Kei Kebreau wrote 8 years ago
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 28384@debbugs.gnu.org)
87tw0ad6hk.fsf@posteo.net
ludo@gnu.org (Ludovic Courtès) writes:

Toggle quote (40 lines)
> Kei Kebreau <kkebreau@posteo.net> skribis:
>
>> ludo@gnu.org (Ludovic Courtès) writes:
>>
>>> Kei Kebreau <kkebreau@posteo.net> skribis:
>>>
>>>> ludo@gnu.org (Ludovic Courtès) writes:
>>>>
>>>>> Hi Kei,
>>>>>
>>>>> The subject is truncated. :-) Caused by which commit?
>>>>>
>>>>> Kei Kebreau <kkebreau@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.

Toggle quote (25 lines)
>>>> From 87ea8addad973568d8599fb93c8df9766b96b6a1 Mon Sep 17 00:00:00 2001
>>>> From: Kei Kebreau <kkebreau@posteo.net>
>>>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>>>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>>>> To: guix-patches@gnu.org
>>>
>>> Wrong patch. :-)
>>>
>>> Ludo’.
>>
>> Fixed!
>>
>> From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
>> From: Kei Kebreau <kkebreau@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.

Toggle quote (4 lines)
> Thanks!
>
> Ludo’.

Thanks for helping to sort this out!
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Ludovic Courtès wrote 8 years ago
(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 28384@debbugs.gnu.org)
87o9qi5lvj.fsf@gnu.org
Kei Kebreau <kkebreau@posteo.net> skribis:

Toggle quote (73 lines)
> ludo@gnu.org (Ludovic Courtès) writes:
>
>> Kei Kebreau <kkebreau@posteo.net> skribis:
>>
>>> ludo@gnu.org (Ludovic Courtès) writes:
>>>
>>>> Kei Kebreau <kkebreau@posteo.net> skribis:
>>>>
>>>>> ludo@gnu.org (Ludovic Courtès) writes:
>>>>>
>>>>>> Hi Kei,
>>>>>>
>>>>>> The subject is truncated. :-) Caused by which commit?
>>>>>>
>>>>>> Kei Kebreau <kkebreau@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@posteo.net>
>>>>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>>>>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>>>>> To: guix-patches@gnu.org
>>>>
>>>> Wrong patch. :-)
>>>>
>>>> Ludo’.
>>>
>>> Fixed!
>>>
>>> From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
>>> From: Kei Kebreau <kkebreau@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'.
Kei Kebreau wrote 8 years ago
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 28384-done@debbugs.gnu.org)
87h8wachr4.fsf@posteo.net
ludo@gnu.org (Ludovic Courtès) writes:

Toggle quote (80 lines)
> Kei Kebreau <kkebreau@posteo.net> skribis:
>
>> ludo@gnu.org (Ludovic Courtès) writes:
>>
>>> Kei Kebreau <kkebreau@posteo.net> skribis:
>>>
>>>> ludo@gnu.org (Ludovic Courtès) writes:
>>>>
>>>>> Kei Kebreau <kkebreau@posteo.net> skribis:
>>>>>
>>>>>> ludo@gnu.org (Ludovic Courtès) writes:
>>>>>>
>>>>>>> Hi Kei,
>>>>>>>
>>>>>>> The subject is truncated. :-) Caused by which commit?
>>>>>>>
>>>>>>> Kei Kebreau <kkebreau@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@posteo.net>
>>>>>> Date: Sat, 29 Jul 2017 11:28:42 -0400
>>>>>> Subject: [PATCH] gnu: Use 'modify-phases' syntax.
>>>>>> To: guix-patches@gnu.org
>>>>>
>>>>> Wrong patch. :-)
>>>>>
>>>>> Ludo’.
>>>>
>>>> Fixed!
>>>>
>>>> From d9eee184cf80252092c34864d492527ee768a7fb Mon Sep 17 00:00:00 2001
>>>> From: Kei Kebreau <kkebreau@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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