This fixes some uses of wrap-script.
From c451edc7ba759cf31f5d0ca113f7df9e28ccfe3b Mon Sep 17 00:00:00 2001 From: Maxime Devos <[email protected]> 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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