From: Maxime Devos <maximedevos@telenet.be>
To: "Ludovic Courtès" <ludo@gnu.org>
Cc: 47221@debbugs.gnu.org
Subject: bug#47221: Guile not in native-inputs when it should
Date: Thu, 18 Mar 2021 15:01:59 +0100 [thread overview]
Message-ID: <81fb51c76013333b8080893491ce298ed55e93f5.camel@telenet.be> (raw)
In-Reply-To: <c34c473b38b2c659947d684d357a31a2a3ece480.camel@telenet.be>
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This fixes some uses of wrap-script.
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From c451edc7ba759cf31f5d0ca113f7df9e28ccfe3b Mon Sep 17 00:00:00 2001
From: Maxime Devos <maximedevos@telenet.be>
Date: Thu, 18 Mar 2021 14:40:20 +0100
Subject: [PATCH] gnu: Explicitely pass the guile binary to wrap-script.
If the #:guile argument of wrap-script is not set,
then a guile binary will be searched for in the PATH.
When cross-compiling, this would result in a guile package
compiled for a wrong architecture being used (if guile is in
native-inputs) or a broken wrapper script that tries to use
"#f" as interpreter.
Note that there are more cross-compilation issues
lurking in the affected packages, e.g. gess uses a
python of the incorrect architecture.
Partially fixes: <https://issues.guix.gnu.org/47221>.
* gnu/packages/xdisorg.scm (clipmenu)[arguments]: Use the
guile of the target platform in wrap-script.
* gnu/packages/vpn.scm (vpnc-scripts)[arguments]: Likewise.
* gnu/packages/mail.scm (sieve-connect)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm
(proteinortho)[arguments]: Likewise.
(prinseq)[arguments]: Likewise.
(gess)[arguments]: Likewise.
(nanopolish)[arguments]: Likewise.
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++--------
gnu/packages/mail.scm | 4 +++-
gnu/packages/vpn.scm | 2 ++
gnu/packages/xdisorg.scm | 4 +++-
4 files changed, 27 insertions(+), 10 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8b38c7ce0d..eb9355a37e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5426,10 +5426,13 @@ predicts the locations of structural units in the sequences.")
#t))
(add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((path (getenv "PATH"))
- (out (assoc-ref outputs "out")))
+ (let* ((path (getenv "PATH"))
+ (out (assoc-ref outputs "out"))
+ (guile (assoc-ref inputs "guile")))
(for-each (lambda (script)
- (wrap-script script `("PATH" ":" prefix (,path))))
+ (wrap-script script
+ #:guile (string-append guile "/bin/guile")
+ `("PATH" ":" prefix (,path))))
(cons (string-append out "/bin/proteinortho")
(find-files out "\\.(pl|py)$"))))
#t)))))
@@ -7900,11 +7903,14 @@ experience substantial biological insertions and deletions.")
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
+ (bin (string-append out "/bin"))
+ (guile (assoc-ref inputs "guile"))
+ (guile-binary (string-append guile "/bin/guile")))
(for-each (lambda (file)
(chmod file #o555)
(install-file file bin)
(wrap-script (string-append bin "/" (basename file))
+ #:guile guile-binary
`("PERL5LIB" ":" prefix
(,(getenv "PERL5LIB")))))
(find-files "." "prinseq.*.pl"))))))))
@@ -11123,7 +11129,8 @@ remove biased methylation positions for RRBS sequence files.")
out "/lib/python"
,(version-major+minor
(package-version python))
- "/site-packages/gess/")))
+ "/site-packages/gess/"))
+ (guile (assoc-ref inputs "guile")))
(mkdir-p target)
(copy-recursively "." target)
;; Make GESS.py executable
@@ -11138,6 +11145,7 @@ matplotlib.use('Agg')
" line)))
;; Make sure GESS has all modules in its path
(wrap-script (string-append target "GESS.py")
+ #:guile (string-append guile "/bin/guile")
`("PYTHONPATH" ":" = (,target ,(getenv "PYTHONPATH"))))
(mkdir-p bin)
(symlink (string-append target "GESS.py")
@@ -14345,16 +14353,19 @@ choosing which reads pass the filter.")
(find-files "scripts" ".*"))
#t)))
(add-after 'install 'wrap-programs
- (lambda* (#:key outputs #:allow-other-keys)
+ (lambda* (#:key inputs outputs #:allow-other-keys)
(let ((pythonpath (getenv "PYTHONPATH"))
(perl5lib (getenv "PERL5LIB"))
(scripts (string-append (assoc-ref outputs "out")
- "/share/nanopolish/scripts")))
+ "/share/nanopolish/scripts"))
+ (guile (assoc-ref inputs "guile")))
(for-each (lambda (file)
(wrap-program file `("PYTHONPATH" ":" prefix (,pythonpath))))
(find-files scripts "\\.py"))
(for-each (lambda (file)
- (wrap-script file `("PERL5LIB" ":" prefix (,perl5lib))))
+ (wrap-script file
+ #:guile (string-append guile "/bin/guile")
+ `("PERL5LIB" ":" prefix (,perl5lib))))
(find-files scripts "\\.pl"))))))))
(inputs
`(("guile" ,guile-3.0) ; for wrappers
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index d21c0e204d..5493d51203 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -2841,8 +2841,10 @@ transfer protocols.")
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
- (path (getenv "PERL5LIB")))
+ (path (getenv "PERL5LIB"))
+ (guile (assoc-ref inputs "guile")))
(wrap-script (string-append out "/bin/sieve-connect")
+ #:guile (string-append guile "/bin/guile")
`("PERL5LIB" ":" = (,path)))
#t))))))
(inputs
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 76af7582fc..8aa1ac672c 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -196,6 +196,8 @@ Only \"Universal TUN/TAP device driver support\" is needed in the kernel.")
(for-each
(lambda (script)
(wrap-script (string-append out "/etc/vpnc/" script)
+ #:guile (string-append (assoc-ref inputs "guile")
+ "/bin/guile")
`("PATH" ":" prefix
,(map (lambda (name)
(let ((input (assoc-ref inputs name)))
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 56ac53edec..5aad1c8cce 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -2545,10 +2545,12 @@ tools to complement clipnotify.")
(gawk (assoc-ref inputs "gawk"))
(util-linux (assoc-ref inputs "util-linux"))
(xdotool (assoc-ref inputs "xdotool"))
- (xsel (assoc-ref inputs "xsel")))
+ (xsel (assoc-ref inputs "xsel"))
+ (guile (assoc-ref inputs "guile")))
(for-each
(lambda (prog)
(wrap-script (string-append out "/bin/" prog)
+ #:guile (string-append guile "/bin/guile")
`("PATH" ":" prefix
,(map (lambda (dir)
(string-append dir "/bin"))
--
2.30.2
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next prev parent reply other threads:[~2021-03-18 14:04 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
[not found] <87y2ewyv7o.fsf@ngyro.com>
[not found] ` <20210309193925.15447-1-samplet@ngyro.com>
[not found] ` <7a04ca46ee7f332e6a31cecbdf9ad4b4133a86f3.camel@telenet.be>
[not found] ` <87zgz1y030.fsf_-_@gnu.org>
2021-03-17 21:58 ` bug#47221: Guile not in native-inputs when it should Maxime Devos
2021-03-18 7:18 ` Maxime Devos
2021-03-18 9:29 ` Maxime Devos
2021-03-18 14:01 ` Maxime Devos [this message]
2021-03-18 19:08 ` Maxime Devos
2021-03-20 21:45 ` bug#47221: [PATCH v2]: Correct some inputs / native-inputs issues with guile Maxime Devos
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