bug#66305: Error with recursive git checkout

bug#66305: Error with recursive git checkout

[Guillaume Le Vaillant]

[-- Attachment #1.1: Type: text/plain, Size: 2545 bytes --]

Hi.

With Guix at 47d0346553fdad9795c9390a60944ccaad7e5255, I'm unable to
build a package (see attached patch) requiring a recursive git-fetch to
get the sources:

--8<---------------cut here---------------start------------->8---
$ ./pre-inst-env guix build bladerf
The following derivations will be built:
  /gnu/store/982zz7z94va89fxn79hpjil5wp0v49pn-bladerf-2023.02.drv
  /gnu/store/5rlqf4srlnnymsv93ydxkgxwgfszkszw-bladerf-2023.02-checkout.drv
building /gnu/store/5rlqf4srlnnymsv93ydxkgxwgfszkszw-bladerf-2023.02-checkout.drv...
Initialized empty Git repository in /gnu/store/fhlm9zxs4r4cgapbngckpzrs8rnzf1l2-bladerf-2023.02-checkout/.git/
From https://github.com/Nuand/bladeRF
 * tag               2023.02    -> FETCH_HEAD
Note: switching to 'FETCH_HEAD'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 41ef634 Revert "libbladeRF: update compatibility for FPGA v0.15.0 from libbladeRF 2.4.0 to 2.5.0"
/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 7: basename: command not found
/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 7: sed: command not found
/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 77: basename: command not found
/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 77: sed: command not found
/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 292: uname: command not found
/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 613: sed: command not found
/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 613: cmd_: command not found
git-fetch: '/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/bin/git submodule update --init --recursive' failed with exit code 127
--8<---------------cut here---------------end--------------->8---

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1.2: 0001-gnu-Add-bladerf.patch --]
[-- Type: text/x-patch, Size: 3029 bytes --]

From ac6fc0fdf16187c4e0c61916c52ced35a031fd76 Mon Sep 17 00:00:00 2001
Message-ID: <ac6fc0fdf16187c4e0c61916c52ced35a031fd76.1696246171.git.glv@posteo.net>
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Sat, 30 Sep 2023 11:17:40 +0200
Subject: [PATCH 1/8] gnu: Add bladerf.

* gnu/packages/radio.scm (bladerf): New variable.
---
 gnu/packages/radio.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 2e4e9db4cc..aa26c04db2 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -69,10 +69,12 @@ (define-module (gnu packages radio)
   #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages javascript)
+  #:use-module (gnu packages libedit)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages logging)
   #:use-module (gnu packages lua)
+  #:use-module (gnu packages man)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages multiprecision)
@@ -1416,6 +1418,43 @@ (define-public hackrf
 @code{(udev-rules-service 'hackrf hackrf #:groups '(\"dialout\"))}.")
     (license license:gpl2)))
 
+(define-public bladerf
+  (package
+    (name "bladerf")
+    (version "2023.02")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Nuand/bladeRF")
+             (commit version)
+             (recursive? #t)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "038v9qdmrwx9mxsrq4l36bap0bsypyg4i8hs7l7srv4b0c2s7ynp"))))
+    (build-system cmake-build-system)
+    (native-inputs (list doxygen help2man pkg-config))
+    (inputs (list libedit libusb))
+    (arguments
+     (list #:configure-flags #~(list "-DTAGGED_RELEASE=ON"
+                                     (string-append "-DUDEV_RULES_PATH="
+                                                    #$output
+                                                    "/lib/udev/rules.d")
+                                     "-DBLADERF_GROUP=dialout"
+                                     "-DBUILD_DOCUMENTATION=ON")
+           #:tests? #f)) ; No test suite
+    (home-page "https://www.nuand.com/")
+    (synopsis "User-space library and utilities for BladeRF SDR")
+    (description
+     "This package contains a library and command line utilities for
+controlling the BladeRF Software Defined Radio (SDR) over USB.  To install the
+hackrf udev rules, you must extend 'udev-service-type' with this package.
+E.g.: @code{(udev-rules-service 'bladerf bladerf)}.")
+    (license (list license:bsd-3
+                   license:expat
+                   license:gpl2+
+                   license:lgpl2.1+))))
+
 (define-public hamlib
   (package
     (name "hamlib")

base-commit: 47d0346553fdad9795c9390a60944ccaad7e5255
-- 
2.41.0


[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 247 bytes --]

bug#66305: Error with recursive git checkout

[Guillaume Le Vaillant]

[-- Attachment #1: Type: text/plain, Size: 184 bytes --]

Workaround: by rebooting the machine to an older generation (and
therefore an older guix-daemon, with Guix at
4f35ff1275e05be31f5d41464ccf147e9dbfd016), the recursive git-fetch
works.

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 247 bytes --]

bug#66305: Error with recursive git checkout

[Simon Tournier]

Hi Guillaume,

On Mon, 02 Oct 2023 at 11:17, Guillaume Le Vaillant <glv@posteo.net> wrote:

> With Guix at 47d0346553fdad9795c9390a60944ccaad7e5255, I'm unable to
> build a package (see attached patch) requiring a recursive git-fetch to
> get the sources:

[...]

> HEAD is now at 41ef634 Revert "libbladeRF: update compatibility for FPGA v0.15.0 from libbladeRF 2.4.0 to 2.5.0"
> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 7: basename: command not found
> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 7: sed: command not found
> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 77: basename: command not found
> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 77: sed: command not found
> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 292: uname: command not found
> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 613: sed: command not found
> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 613: cmd_: command not found
> git-fetch: '/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/bin/git submodule update --init --recursive' failed with exit code 127

It looks very similar as bug#65924:

        bug#65924: git searches coreutils and util-linux commands in PATH
        Maxim Cournoyer <maxim.cournoyer@gmail.com>
        Wed, 13 Sep 2023 14:00:09 -0400
        id:87fs3iuf6e.fsf@gmail.com
        https://issues.guix.gnu.org//65924
        https://issues.guix.gnu.org/msgid/87fs3iuf6e.fsf@gmail.com
        https://yhetil.org/guix/87fs3iuf6e.fsf@gmail.com

I think it is a corollary from:

        bug#65866: [PATCH 0/8] Add built-in builder for Git checkouts
        Ludovic Courtès <ludo@gnu.org>
        Tue, 26 Sep 2023 17:44:22 +0200
        id:87fs312b3d.fsf_-_@gnu.org
        https://issues.guix.gnu.org//65866
        https://issues.guix.gnu.org/msgid/87fs312b3d.fsf_-_@gnu.org
        https://yhetil.org/guix/87fs312b3d.fsf_-_@gnu.org

and if I am correct, such potential issue had been pointed by:

        Re: hard dependency on Git? (was bug#65866: [PATCH 0/8] Add built-in builder for Git checkouts)
        Simon Tournier <zimon.toutoune@gmail.com>
        Thu, 14 Sep 2023 19:28:06 +0200
        id:CAJ3okZ0hzimVNtTcSsJKR-x=WKpPVtHYxshznGzecqxNHFWC5Q@mail.gmail.com
        https://lists.gnu.org/archive/html/guix-devel/2023-09
        https://yhetil.org/guix/CAJ3okZ0hzimVNtTcSsJKR-x=WKpPVtHYxshznGzecqxNHFWC5Q@mail.gmail.com

Cheers,
simon

bug#66305: Error with recursive git checkout

[Ludovic Courtès]

[-- Attachment #1: Type: text/plain, Size: 1886 bytes --]

Hello,

Simon Tournier <zimon.toutoune@gmail.com> skribis:

> On Mon, 02 Oct 2023 at 11:17, Guillaume Le Vaillant <glv@posteo.net> wrote:
>
>> With Guix at 47d0346553fdad9795c9390a60944ccaad7e5255, I'm unable to
>> build a package (see attached patch) requiring a recursive git-fetch to
>> get the sources:
>
> [...]
>
>> HEAD is now at 41ef634 Revert "libbladeRF: update compatibility for FPGA v0.15.0 from libbladeRF 2.4.0 to 2.5.0"
>> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 7: basename: command not found
>> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 7: sed: command not found
>> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 77: basename: command not found
>> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 77: sed: command not found
>> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-sh-setup: line 292: uname: command not found
>> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 613: sed: command not found
>> /gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/libexec/git-core/git-submodule: line 613: cmd_: command not found
>> git-fetch: '/gnu/store/y3vdq2pdkljrw63xxnc2vb6lz07ycar6-git-minimal-2.41.0/bin/git submodule update --init --recursive' failed with exit code 127
>
> It looks very similar as bug#65924:
>
>         bug#65924: git searches coreutils and util-linux commands in PATH
>         Maxim Cournoyer <maxim.cournoyer@gmail.com>

D’oh!  Thanks Simon and Guillaume for the heads-up (I had totally
overlooked that you raised this during the review, Simon; my bad).

Here’s a patch that fixes it for me:


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: Type: text/x-patch, Size: 801 bytes --]

diff --git a/guix/scripts/perform-download.scm b/guix/scripts/perform-download.scm
index 045dd84ad6..c869f19502 100644
--- a/guix/scripts/perform-download.scm
+++ b/guix/scripts/perform-download.scm
@@ -108,6 +108,10 @@ (define* (perform-git-download drv output
            (drv-output (assoc-ref (derivation-outputs drv) "out"))
            (algo       (derivation-output-hash-algo drv-output))
            (hash       (derivation-output-hash drv-output)))
+      ;; Commands such as 'git submodule' expect Coreutils and sed (among
+      ;; others) to be in $PATH.
+      (setenv "PATH" "/run/current-system/profile/bin:/bin:/usr/bin")
+
       (git-fetch-with-fallback url commit output
                                #:recursive? recursive?
                                #:git-command %git))))

[-- Attachment #3: Type: text/plain, Size: 468 bytes --]


To test it, you need to run the daemon from your checkout, with
something like:

  sudo herd stop guix-daemon
  sudo -E ./pre-inst-env guix-daemon --build-users-group=guixbuild &

(Once we’ve applied the fix, we’ll have to update the ‘guix’ package.)

I think we should eventually our ‘git’ package as discussed in
<https://issues.guix.gnu.org/65924>, but that won’t help on foreign
distros anyway, hence the fix above.

WDYT?

Ludo’.

bug#66305: Error with recursive git checkout

[Simon Tournier]

Hi Ludo,

On Wed, 04 Oct 2023 at 18:25, Ludovic Courtès <ludo@gnu.org> wrote:

> diff --git a/guix/scripts/perform-download.scm b/guix/scripts/perform-download.scm
> index 045dd84ad6..c869f19502 100644
> --- a/guix/scripts/perform-download.scm
> +++ b/guix/scripts/perform-download.scm
> @@ -108,6 +108,10 @@ (define* (perform-git-download drv output
>             (drv-output (assoc-ref (derivation-outputs drv) "out"))
>             (algo       (derivation-output-hash-algo drv-output))
>             (hash       (derivation-output-hash drv-output)))
> +      ;; Commands such as 'git submodule' expect Coreutils and sed (among
> +      ;; others) to be in $PATH.
> +      (setenv "PATH" "/run/current-system/profile/bin:/bin:/usr/bin")
> +
>        (git-fetch-with-fallback url commit output
>                                 #:recursive? recursive?
>                                 #:git-command %git))))

LGTM.

Well, I would add a comment explicitly mentioning that’s a temporary fix
pointing this issue #66305.

And I have tested with:

--8<---------------cut here---------------start------------->8---
$ guix build  ocaml-ansiterminal -S --no-substitutes
$ guix build volk --no-substitutes --check -S
--8<---------------cut here---------------end--------------->8---


Cheers,
simon

bug#66305: Error with recursive git checkout

[Simon Tournier]

On Wed, 4 Oct 2023 at 20:16, Simon Tournier <zimon.toutoune@gmail.com> wrote:

> And I have tested with:

On foreign distro I mean :-)

bug#66305: Error with recursive git checkout

[Ludovic Courtès]

Hello,

Simon Tournier <zimon.toutoune@gmail.com> skribis:

> On Wed, 04 Oct 2023 at 18:25, Ludovic Courtès <ludo@gnu.org> wrote:
>
>> diff --git a/guix/scripts/perform-download.scm b/guix/scripts/perform-download.scm
>> index 045dd84ad6..c869f19502 100644
>> --- a/guix/scripts/perform-download.scm
>> +++ b/guix/scripts/perform-download.scm
>> @@ -108,6 +108,10 @@ (define* (perform-git-download drv output
>>             (drv-output (assoc-ref (derivation-outputs drv) "out"))
>>             (algo       (derivation-output-hash-algo drv-output))
>>             (hash       (derivation-output-hash drv-output)))
>> +      ;; Commands such as 'git submodule' expect Coreutils and sed (among
>> +      ;; others) to be in $PATH.
>> +      (setenv "PATH" "/run/current-system/profile/bin:/bin:/usr/bin")
>> +
>>        (git-fetch-with-fallback url commit output
>>                                 #:recursive? recursive?
>>                                 #:git-command %git))))
>
> LGTM.
>
> Well, I would add a comment explicitly mentioning that’s a temporary fix
> pointing this issue #66305.

It’s not temporary in that it will still be needed for example by the
Debian package of Guix.  But yeah, I’ll clarify that in the comment.

> And I have tested with:
>
> $ guix build  ocaml-ansiterminal -S --no-substitutes
> $ guix build volk --no-substitutes --check -S

Awesome, thanks for checking!

Ludo’.

bug#66305: Error with recursive git checkout

[Ludovic Courtès]

Hi!

Pushed as 762fdbdef52b4c17df578478cadc8655d56171a4.

Now to update ‘guix’…

Ludo’.

bug#66305: Error with recursive git checkout

[Ludovic Courtès]

Ludovic Courtès <ludo@gnu.org> skribis:

> Pushed as 762fdbdef52b4c17df578478cadc8655d56171a4.
>
> Now to update ‘guix’…

Done last week in 16fd9d6e3d626fc624c38cb3096331905a4161e4.

Closing!

bug#66305: Error with recursive git checkout

[Alexis Simon via Bug reports for GNU Guix]

Hi,

I think I'm hitting this bug trying to git-fetch with submodules.
I am on a foreign distro.

--8<---------------cut here---------------start------------->8---
/gnu/store/pmv37cxc4cg1s7x8yg8dkhikkwmwpncr-git-minimal-2.41.0/libexec/git-core/git-submodule: 
line 7: /bin/basename: Permission denied
/gnu/store/pmv37cxc4cg1s7x8yg8dkhikkwmwpncr-git-minimal-2.41.0/libexec/git-core/git-submodule: 
line 7: /bin/sed: Permission denied
/gnu/store/pmv37cxc4cg1s7x8yg8dkhikkwmwpncr-git-minimal-2.41.0/libexec/git-core/git-sh-setup: 
line 77: /bin/basename: Permission denied
/gnu/store/pmv37cxc4cg1s7x8yg8dkhikkwmwpncr-git-minimal-2.41.0/libexec/git-core/git-sh-setup: 
line 77: /bin/sed: Permission denied
/gnu/store/pmv37cxc4cg1s7x8yg8dkhikkwmwpncr-git-minimal-2.41.0/libexec/git-core/git-sh-setup: 
line 292: /bin/uname: Permission denied
/gnu/store/pmv37cxc4cg1s7x8yg8dkhikkwmwpncr-git-minimal-2.41.0/libexec/git-core/git-submodule: 
line 613: /bin/sed: Permission denied
/gnu/store/pmv37cxc4cg1s7x8yg8dkhikkwmwpncr-git-minimal-2.41.0/libexec/git-core/git-submodule: 
line 613 : cmd_: command not found
git-fetch: 
'/gnu/store/pmv37cxc4cg1s7x8yg8dkhikkwmwpncr-git-minimal-2.41.0/bin/git 
submodule update --init --recursive' failed with exit code 127
--8<---------------cut here---------------end--------------->8---

This is with a recent guix I think
--8<---------------cut here---------------start------------->8---
❯ guix describe
Generation 8    oct. 24 2023 21:31:58   (current)
   guix 0074731
     repository URL: https://git.savannah.gnu.org/git/guix.git
     branch: master
     commit: 00747316ee0e1a7962ffe226c727776ba7a8163b
--8<---------------cut here---------------end--------------->8---

Alexis

bug#66305: Error with recursive git checkout

[Alexis Simon via Bug reports for GNU Guix]

ah well it seems this is due to a selinux policy error

--8<---------------cut here---------------start------------->8---
SELinux is preventing git-submodule from execute access on the file 
/usr/bin/sed.

*****  Plugin catchall (100. confidence) suggests 
**************************

If you believe that git-submodule should be allowed execute access on 
the sed file by default.
Then you should report this as a bug.
You can generate a local policy module to allow this access.
Do
allow this access for now by executing:
# ausearch -c 'git-submodule' --raw | audit2allow -M my-gitsubmodule
# semodule -X 300 -i my-gitsubmodule.pp


Additional Information:
Source Context                system_u:system_r:guix_daemon.guix_daemon_t:s0
Target Context                system_u:object_r:bin_t:s0
Target Objects                /usr/bin/sed [ file ]
Source                        git-submodule
Source Path                   git-submodule
Port                          <Unknown>
Host                          xps13
Source RPM Packages
Target RPM Packages           sed-4.8-12.fc38.x86_64
SELinux Policy RPM            selinux-policy-targeted-38.29-1.fc38.noarch
Local Policy RPM
Selinux Enabled               True
Policy Type                   targeted
Enforcing Mode                Enforcing
Host Name                     xps13
Platform                      Linux xps13 6.5.7-200.fc38.x86_64 #1 SMP
                               PREEMPT_DYNAMIC Wed Oct 11 04:07:58 UTC 2023
                               x86_64
Alert Count                   460
First Seen                    2023-10-24 20:20:26 PDT
Last Seen                     2023-10-25 09:44:31 PDT
Local ID                      fa57086c-6738-4eec-8252-3abb66a9e249

Raw Audit Messages
type=AVC msg=audit(1698252271.150:513): avc:  denied  { execute } for 
pid=10644 comm="git-submodule" name="sed" dev="dm-0" ino=261979 
scontext=system_u:system_r:guix_daemon.guix_daemon_t:s0 
tcontext=system_u:object_r:bin_t:s0 tclass=file permissive=0


Hash: git-submodule,guix_daemon.guix_daemon_t,bin_t,file,execute
--8<---------------cut here---------------end--------------->8---

But trying to fix it does not seem to have any effect. I've added this 
to the guix-daemon.cil and re-applied
--8<---------------cut here---------------start------------->8---
(allow guix_daemon_t
        bin_t
        (file (execute)))
--8<---------------cut here---------------end--------------->8---

Alexis

bug#66305: Error with recursive git checkout

[Alexis Simon via Bug reports for GNU Guix]

This is what was needed in the selinux policy to fix the errors

--8<---------------cut here---------------start------------->8---
(allow guix_daemon_t
        bin_t
        (file (execute execute_no_trans map)))
--8<---------------cut here---------------end--------------->8---

Alexis