GNU bug report logs - #65853
[PATCH] gnu: scilab: Fix and hardcode script inputs.

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Package: guix-patches; Reported by: Nicolas Graves <ngraves@HIDDEN>; Keywords: patch; merged with #65856, #65857; dated Sun, 10 Sep 2023 16:20:02 UTC; Maintainer for guix-patches is guix-patches@HIDDEN.
Merged 65853 65856 65857. Request was from Tobias Geerinckx-Rice <me@HIDDEN> to control <at> debbugs.gnu.org. Full text available.

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Subject: [PATCH v2] gnu: scilab: Fix and hardcode script inputs.
Date: Thu, 28 Sep 2023 21:03:10 +0200
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* gnu/packages/maths.scm (scilab): Fix script inputs.
[inputs]: Reorder alphabetically. Add coreutils-minimal, grep, sed.
[arguments](phases): Add phase hardcode-script-inputs.
---
 gnu/packages/maths.scm | 46 +++++++++++++++++++++++++++---------------
 1 file changed, 30 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 62d4adfbd1..f7e1de41f3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8433,22 +8433,25 @@ (define-public scilab
         (base32 "0phg9pn24yw98hbh475ik84dnikf1225b2knh7qbhdbdx6fm2d57"))))
     (build-system gnu-build-system)
     (native-inputs (list pkg-config gfortran))
-    (inputs (list libxml2
+    (inputs (list arpack-ng
+                  coreutils-minimal
+                  curl
+                  fftw
+                  gettext-minimal
+                  grep
+                  hdf5-1.8
+                  lapack
+                  libxml2
+                  libx11
+                  matio
+                  openblas
                   `(,pcre "bin")
                   `(,pcre "out")
                   readline
-                  hdf5-1.8
-                  curl
-                  openblas
-                  lapack
-                  arpack-ng
-                  fftw
-                  gettext-minimal
+                  sed
                   suitesparse-3
                   tcl
-                  tk
-                  libx11
-                  matio))
+                  tk))
     (arguments
      `(#:tests? #f
        #:configure-flags
@@ -8484,10 +8487,6 @@ (define-public scilab
        ,#~(modify-phases %standard-phases
             (add-before 'build 'pre-build
               (lambda _
-                ;; Fix scilab script.
-                (substitute* "bin/scilab"
-                  (("\\/bin\\/ls")
-                   (which "ls")))
                 ;; Fix core.start.
                 (substitute* "modules/core/etc/core.start"
                   (("'SCI/modules")
@@ -8519,7 +8518,22 @@ (define-public scilab
                   (("if \\(array_size > 0\\)")
                    "if (*array_size > 0)"))
                 ;; Set SCIHOME to /tmp before macros compilation.
-                (setenv "SCIHOME" "/tmp"))))))
+                (setenv "SCIHOME" "/tmp")))
+            (add-after 'install 'hardcode-script-inputs
+              (lambda _
+                (substitute* (string-append #$output "/bin/scilab")
+                  (("grep")
+                   (search-inputs-file #$inputs "/bin/grep"))
+                  ((" sed ")  ; some "sed" strings are not binaries invocations
+                   (string-append " " (search-inputs-file #$inputs "/bin/sed") " "))
+                  (("/bin/ls")
+                   (search-inputs-file #$inputs "/bin/ls"))
+                  (("uname")
+                   (search-inputs-file #$inputs "/bin/uname"))
+                  (("dirname")
+                   (search-inputs-file #$inputs "/bin/dirname"))
+                  (("basename")
+                   (search-inputs-file #$inputs "/bin/basename"))))))))
     (home-page "https://scilab.org")
     (synopsis "Software for engineers and scientists")
     (description "This package provides the non-graphical version of the Scilab

base-commit: f9784991eb6c7ec1a20f76d080873a3319be0908
-- 
2.41.0





Information forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, guix-patches@HIDDEN:
bug#65853; Package guix-patches. Full text available.

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From: Nicolas Graves <ngraves@HIDDEN>
To: Efraim Flashner <efraim@HIDDEN>
Subject: Re: [bug#65853] [PATCH] gnu: scilab: Fix and hardcode script inputs.
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On 2023-09-28 19:36, Efraim Flashner wrote:

> A couple of things I noticed:
>
> On Sun, Sep 10, 2023 at 06:18:42PM +0200, Nicolas Graves wrote:
>> +                  coreutils
>
> This can be coreutils-minimal
>

Will change it.
>> +                  (("grep")
>> +                   #$(file-append (this-package-input "grep") "/bin/grep"))
>
> These can be (search-input-file #$inputs "/bin/grep") to make it easier
> to swap out the packages for something else if people want.
>

Fine for me.

>> +                  (("sed")
>
> I checked the script, it should be ((" sed ") since there are a couple
> of instances of 'sed' in the script which aren't invocations of sed.

Yes I indeed noticed it too, probably forgot to resubmit a patch but my
local version works well.
>
>> +                   #$(file-append (this-package-input "sed") "/bin/sed"))
>> +                  (("uname")
>> +                   #$(file-append (this-package-input "coreutils")
>> +                                  "/bin/uname"))
>> +                  (("dirname")
>> +                   #$(file-append (this-package-input "coreutils")
>> +                                  "/bin/dirname"))
>> +                  (("basename")
>> +                   #$(file-append (this-package-input "coreutils")
>> +                                  "/bin/basename"))))))))
>
> Are there more binaries which should be substituted? I saw glxgears,
> chcon, a couple instances of java, pwd, valgrind, docbook paths. And
> then there's a couple of other scripts and binaries in the bin/ folder.
> I think it'd be better to use wrap-script or wrap-program and then use
> substitute* to strip the leading /usr/bin/ from the different calls to
> the different binaries.

I don't use more than that for a CLI usage. The thing is that we already
build without the GUI (so without java). Maybe valgrind could be useful
for debugging, docbook for documentation...

I'll take a look in the coming weeks, but I can guarantee it works for
me, so I propose we should process with this one, and add other patches
on top when someone needs them. But we should be mindful that all
possible paths / binaries are not reachable when the script is run
(IIRC, they also depend on the OS and options).

-- 
Best regards,
Nicolas Graves




Information forwarded to guix-patches@HIDDEN:
bug#65853; Package guix-patches. Full text available.

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Date: Thu, 28 Sep 2023 19:36:23 +0300
From: Efraim Flashner <efraim@HIDDEN>
To: Nicolas Graves <ngraves@HIDDEN>
Subject: Re: [bug#65853] [PATCH] gnu: scilab: Fix and hardcode script inputs.
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A couple of things I noticed:

On Sun, Sep 10, 2023 at 06:18:42PM +0200, Nicolas Graves wrote:
> * gnu/packages/maths.scm (scilab): Fix script inputs.
> [inputs]: Reorder alphabetically. Add coreutils, grep, sed.
> [arguments](phases): Add phase hardcode-script-inputs.
> ---
>  gnu/packages/maths.scm | 43 ++++++++++++++++++++++++++++++------------
>  1 file changed, 31 insertions(+), 12 deletions(-)
>=20
> diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
> index 38e71e18f8..40883d71c1 100644
> --- a/gnu/packages/maths.scm
> +++ b/gnu/packages/maths.scm
> @@ -8448,22 +8448,25 @@ (define-public scilab
>          (base32 "0phg9pn24yw98hbh475ik84dnikf1225b2knh7qbhdbdx6fm2d57"))=
))
>      (build-system gnu-build-system)
>      (native-inputs (list pkg-config gfortran))
> -    (inputs (list libxml2
> +    (inputs (list arpack-ng
> +                  coreutils

This can be coreutils-minimal

> +                  curl
> +                  fftw
> +                  gettext-minimal
> +                  grep
> +                  hdf5-1.8
> +                  lapack
> +                  libxml2
> +                  libx11
> +                  matio
> +                  openblas
>                    `(,pcre "bin")
>                    `(,pcre "out")
>                    readline
> -                  hdf5-1.8
> -                  curl
> -                  openblas
> -                  lapack
> -                  arpack-ng
> -                  fftw
> -                  gettext-minimal
> +                  sed
>                    suitesparse-3
>                    tcl
> -                  tk
> -                  libx11
> -                  matio))
> +                  tk))
>      (arguments
>       `(#:tests? #f
>         #:configure-flags
> @@ -8534,7 +8537,23 @@ (define-public scilab
>                    (("if \\(array_size > 0\\)")
>                     "if (*array_size > 0)"))
>                  ;; Set SCIHOME to /tmp before macros compilation.
> -                (setenv "SCIHOME" "/tmp"))))))
> +                (setenv "SCIHOME" "/tmp")))
> +            (add-after 'install 'hardcode-script-inputs
> +              (lambda _
> +                (substitute* (string-append #$output "/bin/scilab")
> +                  (("grep")
> +                   #$(file-append (this-package-input "grep") "/bin/grep=
"))

These can be (search-input-file #$inputs "/bin/grep") to make it easier
to swap out the packages for something else if people want.

> +                  (("sed")

I checked the script, it should be ((" sed ") since there are a couple
of instances of 'sed' in the script which aren't invocations of sed.

> +                   #$(file-append (this-package-input "sed") "/bin/sed"))
> +                  (("uname")
> +                   #$(file-append (this-package-input "coreutils")
> +                                  "/bin/uname"))
> +                  (("dirname")
> +                   #$(file-append (this-package-input "coreutils")
> +                                  "/bin/dirname"))
> +                  (("basename")
> +                   #$(file-append (this-package-input "coreutils")
> +                                  "/bin/basename"))))))))

Are there more binaries which should be substituted? I saw glxgears,
chcon, a couple instances of java, pwd, valgrind, docbook paths. And
then there's a couple of other scripts and binaries in the bin/ folder.
I think it'd be better to use wrap-script or wrap-program and then use
substitute* to strip the leading /usr/bin/ from the different calls to
the different binaries.

>      (home-page "https://scilab.org")
>      (synopsis "Software for engineers and scientists")
>      (description "This package provides the non-graphical version of the=
 Scilab
>=20
> base-commit: 2eb6df537c36da8bf8e81ff698421f6fb1bfd1ab
> prerequisite-patch-id: eb618ab7b10483d917c308a38792af98baa517e2
> prerequisite-patch-id: 40b6c9f09f27833367a71ec25d77afae4d2a835e
> prerequisite-patch-id: c12968d02d99c253f858586a86b16fa32d41f1c1
> prerequisite-patch-id: 09d995d48139f8e61183d5634cda13a01cdb50f7
> prerequisite-patch-id: 86baa45ec2aad977c8c8135f7613aa391155de6d
> prerequisite-patch-id: 3425fbbff6a603d60b4e143ea2141aabf4ddc92c
> prerequisite-patch-id: c373c01aab5dcba3503a97d51c62a595147a041c
> prerequisite-patch-id: cda857c790b88c681c4e713c5f71e40291970daf
> prerequisite-patch-id: 8e234d0f4d93d2aad499eec8842be3d28da98707
> prerequisite-patch-id: 5f664cb2fd995a53765c5ffc19a708ac795cc0c4
> prerequisite-patch-id: ed447cba9cf9b7e1a1b47aa27acb14f8f2da0a8e
> prerequisite-patch-id: 9f80c5bbbfb8cd3347951c4d57634e93ffa79924
> prerequisite-patch-id: 1aaa9f0d466e2d6837f75844df48a98beb70ff24
> prerequisite-patch-id: 34502820d8c0355b3ed2638c457084edeaba029d
> prerequisite-patch-id: a96258da9e78cfb9ac9893cdcdeb38b69b75f134
> --=20
> 2.41.0
>=20
>=20
>=20

--=20
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=D7=9D=D7=99=D7=A8=D7=A4=D7=90
GPG key =3D A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

--6ZT+OmuJDgJ9uoeU
Content-Type: application/pgp-signature; name="signature.asc"

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--6ZT+OmuJDgJ9uoeU--




Information forwarded to guix-patches@HIDDEN:
bug#65853; Package guix-patches. Full text available.
Merged 65853 65856 65857. Request was from Nicolas Graves <ngraves@HIDDEN> to control <at> debbugs.gnu.org. Full text available.

Message received at submit <at> debbugs.gnu.org:


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From: Nicolas Graves <ngraves@HIDDEN>
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Subject: [PATCH] gnu: scilab: Fix and hardcode script inputs.
Date: Sun, 10 Sep 2023 18:18:42 +0200
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* gnu/packages/maths.scm (scilab): Fix script inputs.
[inputs]: Reorder alphabetically. Add coreutils, grep, sed.
[arguments](phases): Add phase hardcode-script-inputs.
---
 gnu/packages/maths.scm | 43 ++++++++++++++++++++++++++++++------------
 1 file changed, 31 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 38e71e18f8..40883d71c1 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8448,22 +8448,25 @@ (define-public scilab
         (base32 "0phg9pn24yw98hbh475ik84dnikf1225b2knh7qbhdbdx6fm2d57"))))
     (build-system gnu-build-system)
     (native-inputs (list pkg-config gfortran))
-    (inputs (list libxml2
+    (inputs (list arpack-ng
+                  coreutils
+                  curl
+                  fftw
+                  gettext-minimal
+                  grep
+                  hdf5-1.8
+                  lapack
+                  libxml2
+                  libx11
+                  matio
+                  openblas
                   `(,pcre "bin")
                   `(,pcre "out")
                   readline
-                  hdf5-1.8
-                  curl
-                  openblas
-                  lapack
-                  arpack-ng
-                  fftw
-                  gettext-minimal
+                  sed
                   suitesparse-3
                   tcl
-                  tk
-                  libx11
-                  matio))
+                  tk))
     (arguments
      `(#:tests? #f
        #:configure-flags
@@ -8534,7 +8537,23 @@ (define-public scilab
                   (("if \\(array_size > 0\\)")
                    "if (*array_size > 0)"))
                 ;; Set SCIHOME to /tmp before macros compilation.
-                (setenv "SCIHOME" "/tmp"))))))
+                (setenv "SCIHOME" "/tmp")))
+            (add-after 'install 'hardcode-script-inputs
+              (lambda _
+                (substitute* (string-append #$output "/bin/scilab")
+                  (("grep")
+                   #$(file-append (this-package-input "grep") "/bin/grep"))
+                  (("sed")
+                   #$(file-append (this-package-input "sed") "/bin/sed"))
+                  (("uname")
+                   #$(file-append (this-package-input "coreutils")
+                                  "/bin/uname"))
+                  (("dirname")
+                   #$(file-append (this-package-input "coreutils")
+                                  "/bin/dirname"))
+                  (("basename")
+                   #$(file-append (this-package-input "coreutils")
+                                  "/bin/basename"))))))))
     (home-page "https://scilab.org")
     (synopsis "Software for engineers and scientists")
     (description "This package provides the non-graphical version of the Scilab

base-commit: 2eb6df537c36da8bf8e81ff698421f6fb1bfd1ab
prerequisite-patch-id: eb618ab7b10483d917c308a38792af98baa517e2
prerequisite-patch-id: 40b6c9f09f27833367a71ec25d77afae4d2a835e
prerequisite-patch-id: c12968d02d99c253f858586a86b16fa32d41f1c1
prerequisite-patch-id: 09d995d48139f8e61183d5634cda13a01cdb50f7
prerequisite-patch-id: 86baa45ec2aad977c8c8135f7613aa391155de6d
prerequisite-patch-id: 3425fbbff6a603d60b4e143ea2141aabf4ddc92c
prerequisite-patch-id: c373c01aab5dcba3503a97d51c62a595147a041c
prerequisite-patch-id: cda857c790b88c681c4e713c5f71e40291970daf
prerequisite-patch-id: 8e234d0f4d93d2aad499eec8842be3d28da98707
prerequisite-patch-id: 5f664cb2fd995a53765c5ffc19a708ac795cc0c4
prerequisite-patch-id: ed447cba9cf9b7e1a1b47aa27acb14f8f2da0a8e
prerequisite-patch-id: 9f80c5bbbfb8cd3347951c4d57634e93ffa79924
prerequisite-patch-id: 1aaa9f0d466e2d6837f75844df48a98beb70ff24
prerequisite-patch-id: 34502820d8c0355b3ed2638c457084edeaba029d
prerequisite-patch-id: a96258da9e78cfb9ac9893cdcdeb38b69b75f134
-- 
2.41.0





Acknowledgement sent to Nicolas Graves <ngraves@HIDDEN>:
New bug report received and forwarded. Copy sent to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, guix-patches@HIDDEN. Full text available.
Report forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, guix-patches@HIDDEN:
bug#65853; Package guix-patches. Full text available.
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