Package: guix-patches;
Reported by: David Elsing <david.elsing <at> posteo.net>
Date: Mon, 3 Oct 2022 00:06:02 UTC
Severity: normal
Tags: patch
Done: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: David Elsing <david.elsing <at> posteo.net> To: Liliana Marie Prikler <liliana.prikler <at> gmail.com>, 58261 <at> debbugs.gnu.org Subject: [bug#58261] [PATCH v2 11/13] gnu: Add avalontoolkit. Date: Thu, 13 Oct 2022 21:01:17 +0000
Liliana Marie Prikler <liliana.prikler <at> gmail.com> writes:
> Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (avalontoolkit): New variable.
>> ---
>> gnu/packages/chemistry.scm | 93
>> ++++++++++++++++++++++++++++++++++++++
>> 1 file changed, 93 insertions(+)
>>
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index 68d28a52c3..e52dd2f3b6 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -928,3 +928,96 @@ (define-public yaehmop
>> (description "@code{YAeHMOP} contains a program and library for
>> performing
>> extended Hückel calculations.")
>> (license license:bsd-2)))
>> +
>> +(define-public avalontoolkit
>> + (package
>> + (name "avalontoolkit")
> I think we could do a hyphen between avalon and toolkit.
>> + (version "1.2.0")
>> + (source
>> + (origin
>> + (method url-fetch)
>> + (uri (string-append
>> + "mirror://sourceforge/avalontoolkit/"
>> + "AvalonToolkit_" (substring version 0 3)
>> "/AvalonToolkit_"
>> + version ".source.tar"))
>> + (sha256
>> + (base32
>> + "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
>> + (modules '((guix build utils) (ice-9 ftw)))
>> + (snippet
>> + #~(begin
>> + (chdir "..")
>> + (delete-file-recursively "SourceDistribution/java")))))
>> + (build-system gnu-build-system)
>> + (arguments
>> + (list
>> + ;; There are no tests
>> + #:tests? #f
>> + #:phases
>> + #~(let ((programs '("canonizer" "matchtest" "smi2mol"
>> "struchk")))
>> + (modify-phases %standard-phases
>> + (delete 'configure)
>> + (add-before 'build 'remove-free
>> + (lambda _
>> + ;; Remove incorrect free of getenv result (patch
>> also in rdkit)
>> + (substitute* "common/reaccsio.c"
>> + (("MyFree.*tempdir.*") ""))))
>> + (replace 'build
>> + (lambda _
>> + (chdir "common")
>> + (let* ((parts
>> + (list
>> + "aacheck" "casutils" "denormal"
>> "depictutil"
>> + "didepict" "fixcharges" "forio" "geometry"
>> "graph"
>> + "hashcode" "layout" "local" "patclean"
>> "pattern"
>> + "perceive" "reaccsio" "rtutils" "set"
>> "shortcut"
>> + "sketch" "ssmatch" "stereo" "symbol_lists"
>> + "symboltable" "utilities"))
>> + (objects (map (lambda (name) (string-append
>> name ".o"))
>> + parts)))
>> + (for-each
>> + (lambda (name)
>> + (display (string-append "Compiling " name
>> ".c\n"))
>> + (invoke "gcc" "-c" "-fPIC" "-O2"
>> + (string-append name ".c")
>> + "-o" (string-append name ".o")))
>> + parts)
>> + (display "Building shared library\n")
>> + (apply invoke "gcc" "-fPIC" "-shared" "-lm"
>> + "-o" "libavalontoolkit.so"
>> + "canonizer.c" "smi2mol.c" "struchk.c"
>> objects)
>> + (for-each
>> + (lambda (program)
>> + (display (string-append "Building " program
>> "\n"))
>> + (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-
>> O2"
>> + (string-append "-Wl,-rpath=" #$output
>> "/lib")
>> + "-DMAIN" (string-append program ".c")
>> "-o" program))
>> + programs))))
> Uhm... is the Makefile that unusable?
Pretty much: Not all programs are built, the compiler and linker options
need to be adjusted in several places and the shared library is missing
some object files. :)
>> + (replace 'install
>> + (lambda _
>> + ;; Executables
>> + (for-each
>> + (lambda (program)
>> + (install-file program (string-append #$output
>> "/bin")))
>> + programs)
>> + (for-each
>> + (lambda (name)
>> + (symlink (string-append #$output "/bin/smi2mol")
>> + (string-append #$output "/bin/" name)))
>> + '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma"
>> "smi2rdf"))
>> + ;; Library
>> + (install-file "libavalontoolkit.so" (string-append
>> #$output "/lib"))
>> + (for-each
>> + (lambda (file)
>> + (install-file file (string-append #$output
>> +
>> "/include/avalontoolkit")))
>> + (find-files "." "\\.h$"))
>> + (install-file "../license.txt"
>> + (string-append #$output "/share/doc/"
>> + #$name "-" #$version
>> "/"))))))))
> Same as above.
There is no install target.
>> + (home-page "https://sourceforge.net/projects/avalontoolkit/")
>> + (synopsis "Tools for SMILES and MOL files and for structure
>> fingerprinting")
>> + (description "This package contains a library and programs for
>> +canonicalization of SMILES and MOL files, molecular structure
>> fingerprinting
>> +and rendering molecules.")
>> + (license license:bsd-3)))
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.