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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47156 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47156@debbugs.gnu.org Cc: zimoun Received: via spool by 47156-submit@debbugs.gnu.org id=B47156.161581332723708 (code B ref 47156); Mon, 15 Mar 2021 13:03:02 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:07 +0000 Received: from localhost ([127.0.0.1]:35049 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrG-0006AC-67 for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:06 -0400 Received: from mail-wr1-f48.google.com ([209.85.221.48]:42396) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr8-00067w-Im for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:59 -0400 Received: by mail-wr1-f48.google.com with SMTP id j2so8628235wrx.9 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:01:58 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=4hxht/01l6LN9BCFmQcL3Tlr6AzFXVEUTCRpq8rUGao=; b=iCGUjpFPbPs3asrIXrP1dweugBzL7MPd6OwZjkmYZpsd2QURO0aEx6UBiusKwWits6 UIu5xL8aGki2s06Qrcav2ccK800eYrRoOF7aPD4YYu2a0RCIkRamWMNO4IDNs7ozamLU bq/zyyNwpbYE3ndIV/EjJVNQ0aFHB8bSINUEZ3NwiQHh+jg9XBtH+ig+TJsS0TEZx+x3 lRAtwlSwqdjvuDyDZo8uNfOkEuMyD/ypcR2ktdV5eBYiYJOrL3BoLgpIBAEJlYB87BRG q3x8s+2tXd1peH9q7QW9ueHwgk70uLj5gvUlfuAZq9CTpDaufnBJiuOTvpO7mywH29HO DAAw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=4hxht/01l6LN9BCFmQcL3Tlr6AzFXVEUTCRpq8rUGao=; b=nBoLWeNHtFnKmwKWu4SJ4JBXJcUJri43nMks0Hm1p/KtMDK6CasArizqAqA4S+a1ea ehrn/srPL2eyOkrNvcb6OgY52DuAoqC7ZnxUkTe4L7LGPCzBbBkp3UFAM1zOZ9X42soM JGKWJog/+oCwaxSdX6FSpXJxqFF14C+bXjFP3Um9udNhzJoK91ITYDcgJljoBg9iSPkw fctMMkSLU8gnIBlq1dGvt1Ssc73nOhoTR7YGAHqvL1exBL3QEbQirtz26wzIy/CIobcc PWw3GMmXA37vwbgy2yNQZqyCtSk8o7j9/rkaFY0iJcmA0uQYtd/tgvdwGy6+1KzPpS2R s8DQ== X-Gm-Message-State: AOAM530pdE/P2hnFMWUPIidaS6u9pmiMBuWIw8WFmQmOmYEvd1+AOLgv phckWXLjiHPWOYUg5J1KE1fX/kbnhqM= X-Google-Smtp-Source: ABdhPJyIMrGXTHOxXDpBE6JPEeBqlC7XxeGdo8LVEhNBhsys1xz1jXTC4lgxx4bO9sySyD4kqdWAvQ== X-Received: by 2002:a5d:6290:: with SMTP id k16mr26167488wru.177.1615813307924; Mon, 15 Mar 2021 06:01:47 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.47 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:47 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:29 +0100 Message-Id: <20210315130134.30302-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210315130134.30302-1-zimon.toutoune@gmail.com> References: <20210315130134.30302-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-bioccheck): Move from here... * gnu/packages/bioconductor.scm (r-bioccheck): ...to here. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 --------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91d02639a3..7c97e52312 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8452,6 +8452,55 @@ microarray data.") monograph.") (license license:artistic2.0))) +(define-public r-bioccheck + (package + (name "r-bioccheck") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocCheck" version)) + (sha256 + (base32 + "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) + (properties + `((upstream-name . "BiocCheck"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; This package can be used by calling BiocCheck() from + ;; within R, or by running R CMD BiocCheck . This phase + ;; makes sure the latter works. For this to work, the BiocCheck + ;; script must be somewhere on the PATH (not the R bin directory). + (add-after 'install 'install-bioccheck-subcommand + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (dest-dir (string-append out "/bin")) + (script-dir + (string-append out "/site-library/BiocCheck/script/"))) + (mkdir-p dest-dir) + (symlink (string-append script-dir "/checkBadDeps.R") + (string-append dest-dir "/checkBadDeps.R")) + (symlink (string-append script-dir "/BiocCheck") + (string-append dest-dir "/BiocCheck"))) + #t))))) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) + ("r-httr" ,r-httr) + ("r-knitr" ,r-knitr) + ("r-optparse" ,r-optparse) + ("r-biocmanager" ,r-biocmanager) + ("r-biocviews" ,r-biocviews) + ("r-stringdist" ,r-stringdist))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocCheck") + (synopsis "Executes Bioconductor-specific package checks") + (description "This package contains tools to perform additional quality +checks on R packages that are to be submitted to the Bioconductor repository.") + (license license:artistic2.0))) + (define-public r-biocgraph (package (name "r-biocgraph") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ad3ae204e1..d8d64818d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,55 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-bioccheck - (package - (name "r-bioccheck") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocCheck" version)) - (sha256 - (base32 - "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) - (properties - `((upstream-name . "BiocCheck"))) - (build-system r-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - ;; This package can be used by calling BiocCheck() from - ;; within R, or by running R CMD BiocCheck . This phase - ;; makes sure the latter works. For this to work, the BiocCheck - ;; script must be somewhere on the PATH (not the R bin directory). - (add-after 'install 'install-bioccheck-subcommand - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (dest-dir (string-append out "/bin")) - (script-dir - (string-append out "/site-library/BiocCheck/script/"))) - (mkdir-p dest-dir) - (symlink (string-append script-dir "/checkBadDeps.R") - (string-append dest-dir "/checkBadDeps.R")) - (symlink (string-append script-dir "/BiocCheck") - (string-append dest-dir "/BiocCheck"))) - #t))))) - (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-optparse" ,r-optparse) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-stringdist" ,r-stringdist))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocCheck") - (synopsis "Executes Bioconductor-specific package checks") - (description "This package contains tools to perform additional quality -checks on R packages that are to be submitted to the Bioconductor repository.") - (license license:artistic2.0))) - (define-public r-s4vectors (package (name "r-s4vectors")