From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: Various improvements to the CRAN importer Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 05 Apr 2017 16:41:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 26373@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.149141042212994 (code B ref -1); Wed, 05 Apr 2017 16:41:01 +0000 Received: (at submit) by debbugs.gnu.org; 5 Apr 2017 16:40:22 +0000 Received: from localhost ([127.0.0.1]:33863 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvnyo-0003NU-53 for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:40:22 -0400 Received: from eggs.gnu.org ([208.118.235.92]:41229) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvnym-0003NI-0I for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:40:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cvnyg-0006oa-4n for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:40:14 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_20 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:42419) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cvnyg-0006oW-2q for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:40:14 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:60429) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cvnyf-0001lC-2h for guix-patches@gnu.org; Wed, 05 Apr 2017 12:40:13 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cvnyb-0006lo-20 for guix-patches@gnu.org; Wed, 05 Apr 2017 12:40:13 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21078) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cvnya-0006kQ-Ps for guix-patches@gnu.org; Wed, 05 Apr 2017 12:40:08 -0400 Received: from localhost (141.80.246.58 [141.80.246.58]) by mx.zohomail.com with SMTPS id 1491410404499940.8845445169707; Wed, 5 Apr 2017 09:40:04 -0700 (PDT) User-agent: mu4e 0.9.18; emacs 25.1.1 From: Ricardo Wurmus X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 05 Apr 2017 18:40:02 +0200 Message-ID: <8737dm3j19.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -4.0 (----) The following patch series improves the CRAN importer. From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 1/6] import cran: Exclude experiment packages in predicate "bioconductor-package?". References: <8737dm3j19.fsf@elephly.net> In-Reply-To: <8737dm3j19.fsf@elephly.net> Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 05 Apr 2017 16:43:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 26373@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.149141053913199 (code B ref 26373); Wed, 05 Apr 2017 16:43:01 +0000 Received: (at 26373) by debbugs.gnu.org; 5 Apr 2017 16:42:19 +0000 Received: from localhost ([127.0.0.1]:33868 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0h-0003Qp-Hd for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:19 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21120) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0f-0003Qf-Pk for 26373@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:18 -0400 Received: from localhost (141.80.246.58 [141.80.246.58]) by mx.zohomail.com with SMTPS id 1491410533639918.6506515060373; Wed, 5 Apr 2017 09:42:13 -0700 (PDT) From: Ricardo Wurmus Date: Wed, 5 Apr 2017 18:42:05 +0200 Message-Id: <20170405164210.29428-1-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * guix/import/cran.scm (bioconductor-package?): Exclude experiment packages, because they cannot be updated with the default bioconductor updater. --- guix/import/cran.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 8e24f6e17..f63d23972 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -429,7 +429,9 @@ dependencies." ;; the Github mirror, so we have to exclude them ;; from the set of bioconductor packages that can be ;; updated automatically. - (not (string-contains uri "/data/annotation/")))))) + (not (string-contains uri "/data/annotation/")) + ;; Experiment packages are in a separate repository. + (not (string-contains uri "/data/experiment/")))))) (and (string-prefix? "r-" (package-name package)) (match (and=> (package-source package) origin-uri) ((? string? uri) -- 2.12.2 From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 2/6] import cran: Add predicate for Bioconductor experiment packages. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 05 Apr 2017 16:43:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 26373@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.149141055013230 (code B ref 26373); Wed, 05 Apr 2017 16:43:02 +0000 Received: (at 26373) by debbugs.gnu.org; 5 Apr 2017 16:42:30 +0000 Received: from localhost ([127.0.0.1]:33872 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0r-0003RK-QG for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:29 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21061) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0q-0003R5-0V for 26373@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:28 -0400 Received: from localhost (141.80.246.58 [141.80.246.58]) by mx.zohomail.com with SMTPS id 1491410543313802.4989871812429; Wed, 5 Apr 2017 09:42:23 -0700 (PDT) From: Ricardo Wurmus Date: Wed, 5 Apr 2017 18:42:06 +0200 Message-Id: <20170405164210.29428-2-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 In-Reply-To: <20170405164210.29428-1-rekado@elephly.net> References: <20170405164210.29428-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * guix/import/cran.scm (bioconductor-experiment-package?): New variable. --- guix/import/cran.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index f63d23972..48ab7355d 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -453,6 +453,19 @@ dependencies." (any predicate uris)) (_ #f))))) +(define (bioconductor-experiment-package? package) + "Return true if PACKAGE is an R experiment package from Bioconductor." + (let ((predicate (lambda (uri) + (and (string-prefix? "http://bioconductor.org" uri) + (string-contains uri "/data/experiment/"))))) + (and (string-prefix? "r-" (package-name package)) + (match (and=> (package-source package) origin-uri) + ((? string? uri) + (predicate uri)) + ((? list? uris) + (any predicate uris)) + (_ #f))))) + (define %cran-updater (upstream-updater (name 'cran) -- 2.12.2 From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 3/6] import cran: Refactor "needs-zlib?". Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 05 Apr 2017 16:43:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 26373@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.149141055113238 (code B ref 26373); Wed, 05 Apr 2017 16:43:02 +0000 Received: (at 26373) by debbugs.gnu.org; 5 Apr 2017 16:42:31 +0000 Received: from localhost ([127.0.0.1]:33874 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0t-0003RS-0m for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:31 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21114) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0q-0003R8-Rm for 26373@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:29 -0400 Received: from localhost (141.80.246.58 [141.80.246.58]) by mx.zohomail.com with SMTPS id 1491410545770855.6724032527375; Wed, 5 Apr 2017 09:42:25 -0700 (PDT) From: Ricardo Wurmus Date: Wed, 5 Apr 2017 18:42:07 +0200 Message-Id: <20170405164210.29428-3-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 In-Reply-To: <20170405164210.29428-1-rekado@elephly.net> References: <20170405164210.29428-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * guix/import/cran.scm (tarball-files-match-pattern?): New procedure. (needs-zlib?): Implement in terms of "tarball-files-match-pattern?". --- guix/import/cran.scm | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 48ab7355d..be3b678cd 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -201,17 +201,16 @@ empty list when the FIELD cannot be found." (check "*.f95") (check "*.f"))) -(define (needs-zlib? tarball) - "Return #T if any of the Makevars files in the src directory of the TARBALL -contain a zlib linker flag." +(define (tarball-files-match-pattern? tarball regexp . file-patterns) + "Return #T if any of the files represented by FILE-PATTERNS in the TARBALL +match the given REGEXP." (call-with-temporary-directory (lambda (dir) - (let ((pattern (make-regexp "-lz"))) + (let ((pattern (make-regexp regexp))) (parameterize ((current-error-port (%make-void-port "rw+"))) - (system* "tar" - "xf" tarball "-C" dir - "--wildcards" - "*/src/Makevars*" "*/src/configure*" "*/configure*")) + (apply system* "tar" + "xf" tarball "-C" dir + `("--wildcards" ,@file-patterns))) (any (lambda (file) (call-with-input-file file (lambda (port) @@ -220,10 +219,16 @@ contain a zlib linker flag." (cond ((eof-object? line) #f) ((regexp-exec pattern line) #t) - (else (loop))))))) - #t) + (else (loop)))))))) (find-files dir)))))) +(define (needs-zlib? tarball) + "Return #T if any of the Makevars files in the src directory of the TARBALL +contain a zlib linker flag." + (tarball-files-match-pattern? + tarball "-lz" + "*/src/Makevars*" "*/src/configure*" "*/configure*")) + (define (description->package repository meta) "Return the `package' s-expression for an R package published on REPOSITORY from the alist META, which was derived from the R package's DESCRIPTION file." -- 2.12.2 From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 4/6] import cran: Check if pkg-config is needed. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 05 Apr 2017 16:43:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 26373@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.149141055313260 (code B ref 26373); Wed, 05 Apr 2017 16:43:03 +0000 Received: (at 26373) by debbugs.gnu.org; 5 Apr 2017 16:42:33 +0000 Received: from localhost ([127.0.0.1]:33878 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0v-0003Rn-8b for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:33 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21019) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0u-0003Ra-Gq for 26373@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:32 -0400 Received: from localhost (141.80.246.58 [141.80.246.58]) by mx.zohomail.com with SMTPS id 1491410548168333.96642832070415; Wed, 5 Apr 2017 09:42:28 -0700 (PDT) From: Ricardo Wurmus Date: Wed, 5 Apr 2017 18:42:08 +0200 Message-Id: <20170405164210.29428-4-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 In-Reply-To: <20170405164210.29428-1-rekado@elephly.net> References: <20170405164210.29428-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * guix/import/cran.scm (needs-pkg-config?): New procedure. (description->package): Use it. --- guix/import/cran.scm | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index be3b678cd..423835637 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -229,6 +229,13 @@ contain a zlib linker flag." tarball "-lz" "*/src/Makevars*" "*/src/configure*" "*/configure*")) +(define (needs-pkg-config? tarball) + "Return #T if any of the Makevars files in the src directory of the TARBALL +reference the pkg-config tool." + (tarball-files-match-pattern? + tarball "pkg-config" + "*/src/Makevars*" "*/src/configure*" "*/configure*")) + (define (description->package repository meta) "Return the `package' s-expression for an R package published on REPOSITORY from the alist META, which was derived from the R package's DESCRIPTION file." @@ -278,11 +285,12 @@ from the alist META, which was derived from the R package's DESCRIPTION file." (build-system r-build-system) ,@(maybe-inputs sysdepends) ,@(maybe-inputs (map guix-name propagate) 'propagated-inputs) - ,@(if (needs-fortran? tarball) - `((native-inputs (,'quasiquote - ,(list "gfortran" - (list 'unquote 'gfortran))))) - '()) + ,@(maybe-inputs + `(,@(if (needs-fortran? tarball) + '("gfortran") '()) + ,@(if (needs-pkg-config? tarball) + '("pkg-config") '())) + 'native-inputs) (home-page ,(if (string-null? home-page) (string-append base-url name) home-page)) -- 2.12.2 From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 5/6] import cran: Ensure substring indices are valid. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 05 Apr 2017 16:43:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 26373@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.149141055313267 (code B ref 26373); Wed, 05 Apr 2017 16:43:03 +0000 Received: (at 26373) by debbugs.gnu.org; 5 Apr 2017 16:42:33 +0000 Received: from localhost ([127.0.0.1]:33880 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0v-0003Rp-FK for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:33 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21052) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0u-0003Rc-Kb for 26373@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:32 -0400 Received: from localhost (141.80.246.58 [141.80.246.58]) by mx.zohomail.com with SMTPS id 149141055065240.4143129730744; Wed, 5 Apr 2017 09:42:30 -0700 (PDT) From: Ricardo Wurmus Date: Wed, 5 Apr 2017 18:42:09 +0200 Message-Id: <20170405164210.29428-5-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 In-Reply-To: <20170405164210.29428-1-rekado@elephly.net> References: <20170405164210.29428-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * guix/import/cran.scm (package->upstream-name): Check that "start" and "end" are valid before using them as substring indices. --- guix/import/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 423835637..557d694ad 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -384,9 +384,10 @@ dependencies." ((or (? string? url) (url _ ...)) (let ((end (string-rindex url #\_)) (start (string-rindex url #\/))) - ;; The URL ends on - ;; (string-append "/" name "_" version ".tar.gz") - (substring url (+ start 1) end))) + (and start end + ;; The URL ends on + ;; (string-append "/" name "_" version ".tar.gz") + (substring url (+ start 1) end)))) (_ #f))) (_ #f))))) -- 2.12.2 From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 6/6] import cran: Skip updating when meta data cannot be downloaded. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 05 Apr 2017 16:43:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 26373@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.149141055813284 (code B ref 26373); Wed, 05 Apr 2017 16:43:04 +0000 Received: (at 26373) by debbugs.gnu.org; 5 Apr 2017 16:42:38 +0000 Received: from localhost ([127.0.0.1]:33883 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo10-0003SC-L9 for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:38 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21006) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvo0y-0003S4-S7 for 26373@debbugs.gnu.org; Wed, 05 Apr 2017 12:42:37 -0400 Received: from localhost (141.80.246.58 [141.80.246.58]) by mx.zohomail.com with SMTPS id 1491410553119134.72032378091546; Wed, 5 Apr 2017 09:42:33 -0700 (PDT) From: Ricardo Wurmus Date: Wed, 5 Apr 2017 18:42:10 +0200 Message-Id: <20170405164210.29428-6-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 In-Reply-To: <20170405164210.29428-1-rekado@elephly.net> References: <20170405164210.29428-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * gnu/packages/bioinformatics.scm (latest-cran-release, latest-bioconductor-release): Abort early when meta data cannot be downloaded. --- guix/import/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 557d694ad..fc7a1ed84 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -398,7 +398,8 @@ dependencies." (package->upstream-name package)) (define meta - (fetch-description 'cran upstream-name)) + (false-if-exception + (fetch-description 'cran upstream-name))) (and meta (let ((version (assoc-ref meta "Version"))) @@ -415,7 +416,8 @@ dependencies." (package->upstream-name package)) (define meta - (fetch-description 'bioconductor upstream-name)) + (false-if-exception + (fetch-description 'bioconductor upstream-name))) (and meta (let ((version (assoc-ref meta "Version"))) -- 2.12.2 From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 1/6] import cran: Exclude experiment packages in predicate "bioconductor-package?". Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 09:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.14918178523789 (code B ref 26373); Mon, 10 Apr 2017 09:51:02 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 09:50:52 +0000 Received: from localhost ([127.0.0.1]:40584 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxVyG-0000z3-4D for submit@debbugs.gnu.org; Mon, 10 Apr 2017 05:50:52 -0400 Received: from eggs.gnu.org ([208.118.235.92]:50669) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxVyE-0000ym-50 for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:50:50 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxVy4-0007J2-0q for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:50:45 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36348) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxVy3-0007Iy-Sf; Mon, 10 Apr 2017 05:50:39 -0400 Received: from [193.50.110.120] (port=50154 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxVy3-0005Ut-Bj; Mon, 10 Apr 2017 05:50:39 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <8737dm3j19.fsf@elephly.net> <20170405164210.29428-1-rekado@elephly.net> Date: Mon, 10 Apr 2017 11:50:37 +0200 In-Reply-To: <20170405164210.29428-1-rekado@elephly.net> (Ricardo Wurmus's message of "Wed, 5 Apr 2017 18:42:05 +0200") Message-ID: <87zifoeglu.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus skribis: > * guix/import/cran.scm (bioconductor-package?): Exclude experiment packages, > because they cannot be updated with the default bioconductor updater. OK. From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 2/6] import cran: Add predicate for Bioconductor experiment packages. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 09:52:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.14918179113933 (code B ref 26373); Mon, 10 Apr 2017 09:52:02 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 09:51:51 +0000 Received: from localhost ([127.0.0.1]:40591 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxVzD-00011M-Es for submit@debbugs.gnu.org; Mon, 10 Apr 2017 05:51:51 -0400 Received: from eggs.gnu.org ([208.118.235.92]:51137) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxVzB-000117-1p for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:51:49 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxVz1-0007rx-57 for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:51:44 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36361) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxVz1-0007rt-1Q; Mon, 10 Apr 2017 05:51:39 -0400 Received: from [193.50.110.120] (port=50162 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxVz0-0005Yg-GF; Mon, 10 Apr 2017 05:51:38 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-2-rekado@elephly.net> Date: Mon, 10 Apr 2017 11:51:36 +0200 In-Reply-To: <20170405164210.29428-2-rekado@elephly.net> (Ricardo Wurmus's message of "Wed, 5 Apr 2017 18:42:06 +0200") Message-ID: <87vaqcegk7.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus skribis: > * guix/import/cran.scm (bioconductor-experiment-package?): New variable. It seems to be a private and unused procedure. Is it really needed? :-) Thanks, Ludo=E2=80=99. From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 3/6] import cran: Refactor "needs-zlib?". Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 09:53:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.14918179334002 (code B ref 26373); Mon, 10 Apr 2017 09:53:01 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 09:52:13 +0000 Received: from localhost ([127.0.0.1]:40595 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxVzZ-00012T-MX for submit@debbugs.gnu.org; Mon, 10 Apr 2017 05:52:13 -0400 Received: from eggs.gnu.org ([208.118.235.92]:51250) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxVzY-00012H-IV for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:52:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxVzQ-00083w-VK for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:52:07 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36364) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxVzQ-00083r-Rz; Mon, 10 Apr 2017 05:52:04 -0400 Received: from [193.50.110.120] (port=50166 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxVzQ-0005an-9M; Mon, 10 Apr 2017 05:52:04 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-3-rekado@elephly.net> Date: Mon, 10 Apr 2017 11:52:02 +0200 In-Reply-To: <20170405164210.29428-3-rekado@elephly.net> (Ricardo Wurmus's message of "Wed, 5 Apr 2017 18:42:07 +0200") Message-ID: <87r310egjh.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus skribis: > * guix/import/cran.scm (tarball-files-match-pattern?): New procedure. > (needs-zlib?): Implement in terms of "tarball-files-match-pattern?". LGTM! From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 4/6] import cran: Check if pkg-config is needed. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 09:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.14918179494033 (code B ref 26373); Mon, 10 Apr 2017 09:53:02 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 09:52:29 +0000 Received: from localhost ([127.0.0.1]:40598 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxVzo-00012y-TL for submit@debbugs.gnu.org; Mon, 10 Apr 2017 05:52:29 -0400 Received: from eggs.gnu.org ([208.118.235.92]:51355) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxVzn-00012m-Qx for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:52:28 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxVzi-00087V-1A for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:52:22 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36369) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxVzh-00087R-U4; Mon, 10 Apr 2017 05:52:21 -0400 Received: from [193.50.110.120] (port=50176 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxVzh-0005dM-97; Mon, 10 Apr 2017 05:52:21 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-4-rekado@elephly.net> Date: Mon, 10 Apr 2017 11:52:19 +0200 In-Reply-To: <20170405164210.29428-4-rekado@elephly.net> (Ricardo Wurmus's message of "Wed, 5 Apr 2017 18:42:08 +0200") Message-ID: <87mvboegj0.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus skribis: > * guix/import/cran.scm (needs-pkg-config?): New procedure. > (description->package): Use it. LGTM! From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 5/6] import cran: Ensure substring indices are valid. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 09:54:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.14918179934138 (code B ref 26373); Mon, 10 Apr 2017 09:54:01 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 09:53:13 +0000 Received: from localhost ([127.0.0.1]:40603 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxW0X-00014f-4h for submit@debbugs.gnu.org; Mon, 10 Apr 2017 05:53:13 -0400 Received: from eggs.gnu.org ([208.118.235.92]:51540) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxW0V-00014R-OD for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:53:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxW0L-0008FW-Ql for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:53:06 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36371) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxW0L-0008FS-NH; Mon, 10 Apr 2017 05:53:01 -0400 Received: from [193.50.110.120] (port=50180 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxW0L-0005fG-2K; Mon, 10 Apr 2017 05:53:01 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-5-rekado@elephly.net> Date: Mon, 10 Apr 2017 11:52:59 +0200 In-Reply-To: <20170405164210.29428-5-rekado@elephly.net> (Ricardo Wurmus's message of "Wed, 5 Apr 2017 18:42:09 +0200") Message-ID: <87inmceghw.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus skribis: > * guix/import/cran.scm (package->upstream-name): Check that "start" and "end" > are valid before using them as substring indices. LGTM! From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 6/6] import cran: Skip updating when meta data cannot be downloaded. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 09:57:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.14918181644448 (code B ref 26373); Mon, 10 Apr 2017 09:57:02 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 09:56:04 +0000 Received: from localhost ([127.0.0.1]:40609 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxW3H-00019g-LR for submit@debbugs.gnu.org; Mon, 10 Apr 2017 05:56:03 -0400 Received: from eggs.gnu.org ([208.118.235.92]:52317) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxW3G-000195-1Q for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:56:02 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxW36-0000WD-73 for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 05:55:56 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36395) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxW36-0000Vy-38; Mon, 10 Apr 2017 05:55:52 -0400 Received: from [193.50.110.120] (port=50200 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxW35-0005pd-Gk; Mon, 10 Apr 2017 05:55:51 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-6-rekado@elephly.net> Date: Mon, 10 Apr 2017 11:55:49 +0200 In-Reply-To: <20170405164210.29428-6-rekado@elephly.net> (Ricardo Wurmus's message of "Wed, 5 Apr 2017 18:42:10 +0200") Message-ID: <87efx0egd6.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus skribis: > * gnu/packages/bioinformatics.scm (latest-cran-release, > latest-bioconductor-release): Abort early when meta data cannot be downlo= aded. > --- > guix/import/cran.scm | 6 ++++-- > 1 file changed, 4 insertions(+), 2 deletions(-) > > diff --git a/guix/import/cran.scm b/guix/import/cran.scm > index 557d694ad..fc7a1ed84 100644 > --- a/guix/import/cran.scm > +++ b/guix/import/cran.scm > @@ -398,7 +398,8 @@ dependencies." > (package->upstream-name package)) >=20=20 > (define meta > - (fetch-description 'cran upstream-name)) > + (false-if-exception > + (fetch-description 'cran upstream-name))) I would prefer catching only the relevant exception. So I suppose something like: (guard (c ((http-get-error? c) (if (=3D 404 (http-get-error-code c)) #f (raise c)))) (fetch-description 'cran upstream-name)) However I see that =E2=80=98fetch-description=E2=80=99 already does that, s= o what exceptions are we protecting against? Thanks, Ludo=E2=80=99. From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 2/6] import cran: Add predicate for Bioconductor experiment packages. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 13:51:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.14918322421037 (code B ref 26373); Mon, 10 Apr 2017 13:51:01 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 13:50:42 +0000 Received: from localhost ([127.0.0.1]:40711 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxZiM-0000Gf-7k for submit@debbugs.gnu.org; Mon, 10 Apr 2017 09:50:42 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21016) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxZiK-0000GW-PF for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 09:50:41 -0400 Received: from localhost (x4d0cdd2a.dyn.telefonica.de [77.12.221.42]) by mx.zohomail.com with SMTPS id 1491832236738163.98052381125171; Mon, 10 Apr 2017 06:50:36 -0700 (PDT) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-2-rekado@elephly.net> <87vaqcegk7.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.1.1 From: Ricardo Wurmus In-reply-to: <87vaqcegk7.fsf@gnu.org> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Mon, 10 Apr 2017 15:50:33 +0200 Message-ID: <87lgr81idy.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: -1.8 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) Ludovic Courtès writes: > Ricardo Wurmus skribis: > >> * guix/import/cran.scm (bioconductor-experiment-package?): New variable. > > It seems to be a private and unused procedure. Is it really needed? > :-) Oh, it wasn’t supposed to be private. There are three kinds of bioconductor packages: the normal ones, experiment packages, and annotation packages. The latter two cannot be updated the usual way, so they are excluded from “bioconductor-package?”, but I thought that one may still want to be able to distinguish between them. It’s true, though, that there’s nothing that can use “bioconductor-experiment-package?” yet, but it’s possible to add an updater for just the experiment packages. (They use a different SVN repository.) -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 6/6] import cran: Skip updating when meta data cannot be downloaded. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 13:56:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.14918325382206 (code B ref 26373); Mon, 10 Apr 2017 13:56:02 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 13:55:38 +0000 Received: from localhost ([127.0.0.1]:41346 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxZn7-0000ZW-D0 for submit@debbugs.gnu.org; Mon, 10 Apr 2017 09:55:38 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21077) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxZn5-0000ZQ-5N for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 09:55:35 -0400 Received: from localhost (x4d0cdd2a.dyn.telefonica.de [77.12.221.42]) by mx.zohomail.com with SMTPS id 1491832532547479.4455076267742; Mon, 10 Apr 2017 06:55:32 -0700 (PDT) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-6-rekado@elephly.net> <87efx0egd6.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.1.1 From: Ricardo Wurmus In-reply-to: <87efx0egd6.fsf@gnu.org> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Mon, 10 Apr 2017 15:55:29 +0200 Message-ID: <87k26s1i5q.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: -1.8 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) Ludovic Courtès writes: > Ricardo Wurmus skribis: > >> * gnu/packages/bioinformatics.scm (latest-cran-release, >> latest-bioconductor-release): Abort early when meta data cannot be downloaded. >> --- >> guix/import/cran.scm | 6 ++++-- >> 1 file changed, 4 insertions(+), 2 deletions(-) >> >> diff --git a/guix/import/cran.scm b/guix/import/cran.scm >> index 557d694ad..fc7a1ed84 100644 >> --- a/guix/import/cran.scm >> +++ b/guix/import/cran.scm >> @@ -398,7 +398,8 @@ dependencies." >> (package->upstream-name package)) >> >> (define meta >> - (fetch-description 'cran upstream-name)) >> + (false-if-exception >> + (fetch-description 'cran upstream-name))) > > I would prefer catching only the relevant exception. So I suppose > something like: > > (guard (c ((http-get-error? c) > (if (= 404 (http-get-error-code c)) > #f > (raise c)))) > (fetch-description 'cran upstream-name)) > > However I see that ‘fetch-description’ already does that, so what > exceptions are we protecting against? I don’t know what the desired behaviour here is. When updating packages, I think it’s good to keep going. If there’s an error downloading the package meta data I want “meta” to be “#f”, which leads to skipping the update. Without turning errors to “#f” I wasn’t able to just update all packages with “guix refresh -t cran,bioconductor -u”. That said, I don’t like this. I feel that it would be better to add a “--keep-going” option for “refresh” and implement it in the shared updater code rather than here. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 2/6] import cran: Add predicate for Bioconductor experiment packages. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 21:36:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.149186010413229 (code B ref 26373); Mon, 10 Apr 2017 21:36:01 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 21:35:04 +0000 Received: from localhost ([127.0.0.1]:41612 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxgxk-0003RI-15 for submit@debbugs.gnu.org; Mon, 10 Apr 2017 17:35:04 -0400 Received: from eggs.gnu.org ([208.118.235.92]:45147) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxgxi-0003Qm-T5 for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 17:35:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxgxa-0007sm-Np for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 17:34:57 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_40,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:45941) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxgxa-0007si-KO; Mon, 10 Apr 2017 17:34:54 -0400 Received: from reverse-83.fdn.fr ([80.67.176.83]:58450 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxgxa-0008GP-1M; Mon, 10 Apr 2017 17:34:54 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-2-rekado@elephly.net> <87vaqcegk7.fsf@gnu.org> <87lgr81idy.fsf@elephly.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 21 Germinal an 225 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-unknown-linux-gnu Date: Mon, 10 Apr 2017 23:34:51 +0200 In-Reply-To: <87lgr81idy.fsf@elephly.net> (Ricardo Wurmus's message of "Mon, 10 Apr 2017 15:50:33 +0200") Message-ID: <878tn8eykk.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus skribis: > Ludovic Court=C3=A8s writes: > >> Ricardo Wurmus skribis: >> >>> * guix/import/cran.scm (bioconductor-experiment-package?): New variable. >> >> It seems to be a private and unused procedure. Is it really needed? >> :-) > > Oh, it wasn=E2=80=99t supposed to be private. There are three kinds of > bioconductor packages: the normal ones, experiment packages, and > annotation packages. > > The latter two cannot be updated the usual way, so they are excluded > from =E2=80=9Cbioconductor-package?=E2=80=9D, but I thought that one may = still want to > be able to distinguish between them. It=E2=80=99s true, though, that the= re=E2=80=99s > nothing that can use =E2=80=9Cbioconductor-experiment-package?=E2=80=9D y= et, but it=E2=80=99s > possible to add an updater for just the experiment packages. (They use > a different SVN repository.) OK, I see. Make sure to export it, then! :-) Thanks for the explanation, Ludo=E2=80=99. From unknown Sat Aug 16 18:43:07 2025 X-Loop: help-debbugs@gnu.org Subject: bug#26373: [PATCH 6/6] import cran: Skip updating when meta data cannot be downloaded. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Apr 2017 21:38:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 26373 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 26373@debbugs.gnu.org Received: via spool by 26373-submit@debbugs.gnu.org id=B26373.149186026113474 (code B ref 26373); Mon, 10 Apr 2017 21:38:02 +0000 Received: (at 26373) by debbugs.gnu.org; 10 Apr 2017 21:37:41 +0000 Received: from localhost ([127.0.0.1]:41617 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxh0H-0003VG-GH for submit@debbugs.gnu.org; Mon, 10 Apr 2017 17:37:41 -0400 Received: from eggs.gnu.org ([208.118.235.92]:45783) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxh0G-0003V5-LI for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 17:37:40 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxh08-0000ML-GR for 26373@debbugs.gnu.org; Mon, 10 Apr 2017 17:37:35 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:45972) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxh08-0000M5-DJ; Mon, 10 Apr 2017 17:37:32 -0400 Received: from reverse-83.fdn.fr ([80.67.176.83]:58452 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxh07-0005Zh-Np; Mon, 10 Apr 2017 17:37:32 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-6-rekado@elephly.net> <87efx0egd6.fsf@gnu.org> <87k26s1i5q.fsf@elephly.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 21 Germinal an 225 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-unknown-linux-gnu Date: Mon, 10 Apr 2017 23:37:29 +0200 In-Reply-To: <87k26s1i5q.fsf@elephly.net> (Ricardo Wurmus's message of "Mon, 10 Apr 2017 15:55:29 +0200") Message-ID: <8737dgeyg6.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus skribis: > Ludovic Court=C3=A8s writes: > >> Ricardo Wurmus skribis: >> >>> * gnu/packages/bioinformatics.scm (latest-cran-release, >>> latest-bioconductor-release): Abort early when meta data cannot be down= loaded. >>> --- >>> guix/import/cran.scm | 6 ++++-- >>> 1 file changed, 4 insertions(+), 2 deletions(-) >>> >>> diff --git a/guix/import/cran.scm b/guix/import/cran.scm >>> index 557d694ad..fc7a1ed84 100644 >>> --- a/guix/import/cran.scm >>> +++ b/guix/import/cran.scm >>> @@ -398,7 +398,8 @@ dependencies." >>> (package->upstream-name package)) >>> >>> (define meta >>> - (fetch-description 'cran upstream-name)) >>> + (false-if-exception >>> + (fetch-description 'cran upstream-name))) >> >> I would prefer catching only the relevant exception. So I suppose >> something like: >> >> (guard (c ((http-get-error? c) >> (if (=3D 404 (http-get-error-code c)) >> #f >> (raise c)))) >> (fetch-description 'cran upstream-name)) >> >> However I see that =E2=80=98fetch-description=E2=80=99 already does that= , so what >> exceptions are we protecting against? > > I don=E2=80=99t know what the desired behaviour here is. When updating > packages, I think it=E2=80=99s good to keep going. If there=E2=80=99s an= error > downloading the package meta data I want =E2=80=9Cmeta=E2=80=9D to be =E2= =80=9C#f=E2=80=9D, which leads > to skipping the update. > > Without turning errors to =E2=80=9C#f=E2=80=9D I wasn=E2=80=99t able to j= ust update all packages > with =E2=80=9Cguix refresh -t cran,bioconductor -u=E2=80=9D. What was the exception? I think a good approach is to catch precisely the kind of error that we don=E2=80=99t want to see. =E2=80=98false-if-exception=E2=80=99 catches ev= erything and could thus hide genuine errors/bugs (including unbound variables and similar), which sounds undesirable. WDYT? Ludo=E2=80=99. From unknown Sat Aug 16 18:43:07 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Ricardo Wurmus Subject: bug#26373: closed (Re: bug#26373: [PATCH 6/6] import cran: Skip updating when meta data cannot be downloaded.) Message-ID: References: <87shk4a8hr.fsf@elephly.net> <8737dm3j19.fsf@elephly.net> X-Gnu-PR-Message: they-closed 26373 X-Gnu-PR-Package: guix-patches Reply-To: 26373@debbugs.gnu.org Date: Tue, 16 May 2017 19:49:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1494964141-2010-1" This is a multi-part message in MIME format... ------------=_1494964141-2010-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #26373: Various improvements to the CRAN importer which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 26373@debbugs.gnu.org. --=20 26373: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D26373 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1494964141-2010-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 26373-done) by debbugs.gnu.org; 16 May 2017 19:48:24 +0000 Received: from localhost ([127.0.0.1]:49112 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dAiSG-0000Vc-I6 for submit@debbugs.gnu.org; Tue, 16 May 2017 15:48:24 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21019) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dAiSE-0000VU-Ve for 26373-done@debbugs.gnu.org; Tue, 16 May 2017 15:48:23 -0400 Received: from localhost (port-92-200-229-218.dynamic.qsc.de [92.200.229.218]) by mx.zohomail.com with SMTPS id 1494964099949900.5782792561091; Tue, 16 May 2017 12:48:19 -0700 (PDT) References: <20170405164210.29428-1-rekado@elephly.net> <20170405164210.29428-6-rekado@elephly.net> <87efx0egd6.fsf@gnu.org> <87k26s1i5q.fsf@elephly.net> <8737dgeyg6.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#26373: [PATCH 6/6] import cran: Skip updating when meta data cannot be downloaded. In-reply-to: <8737dgeyg6.fsf@gnu.org> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 16 May 2017 21:48:16 +0200 Message-ID: <87shk4a8hr.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 26373-done Cc: 26373-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) Ludovic Courtès writes: > Ricardo Wurmus skribis: > >> Ludovic Courtès writes: >> >>> Ricardo Wurmus skribis: >>> >>>> * gnu/packages/bioinformatics.scm (latest-cran-release, >>>> latest-bioconductor-release): Abort early when meta data cannot be downloaded. >>>> --- >>>> guix/import/cran.scm | 6 ++++-- >>>> 1 file changed, 4 insertions(+), 2 deletions(-) >>>> >>>> diff --git a/guix/import/cran.scm b/guix/import/cran.scm >>>> index 557d694ad..fc7a1ed84 100644 >>>> --- a/guix/import/cran.scm >>>> +++ b/guix/import/cran.scm >>>> @@ -398,7 +398,8 @@ dependencies." >>>> (package->upstream-name package)) >>>> >>>> (define meta >>>> - (fetch-description 'cran upstream-name)) >>>> + (false-if-exception >>>> + (fetch-description 'cran upstream-name))) >>> >>> I would prefer catching only the relevant exception. So I suppose >>> something like: >>> >>> (guard (c ((http-get-error? c) >>> (if (= 404 (http-get-error-code c)) >>> #f >>> (raise c)))) >>> (fetch-description 'cran upstream-name)) >>> >>> However I see that ‘fetch-description’ already does that, so what >>> exceptions are we protecting against? >> >> I don’t know what the desired behaviour here is. When updating >> packages, I think it’s good to keep going. If there’s an error >> downloading the package meta data I want “meta” to be “#f”, which leads >> to skipping the update. >> >> Without turning errors to “#f” I wasn’t able to just update all packages >> with “guix refresh -t cran,bioconductor -u”. > > What was the exception? > > I think a good approach is to catch precisely the kind of error that we > don’t want to see. ‘false-if-exception’ catches everything and could > thus hide genuine errors/bugs (including unbound variables and similar), > which sounds undesirable. > > WDYT? I don’t remember why I wanted this, so I didn’t push this patch. I agree that it’s much better to catch errors precisely. Thanks for the review! I pushed all the other patches (with the exception of one that Mathieu had already implemented independently) to master. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ------------=_1494964141-2010-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 5 Apr 2017 16:40:22 +0000 Received: from localhost ([127.0.0.1]:33863 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvnyo-0003NU-53 for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:40:22 -0400 Received: from eggs.gnu.org ([208.118.235.92]:41229) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvnym-0003NI-0I for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:40:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cvnyg-0006oa-4n for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:40:14 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_20 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:42419) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cvnyg-0006oW-2q for submit@debbugs.gnu.org; Wed, 05 Apr 2017 12:40:14 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:60429) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cvnyf-0001lC-2h for guix-patches@gnu.org; Wed, 05 Apr 2017 12:40:13 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cvnyb-0006lo-20 for guix-patches@gnu.org; Wed, 05 Apr 2017 12:40:13 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21078) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cvnya-0006kQ-Ps for guix-patches@gnu.org; Wed, 05 Apr 2017 12:40:08 -0400 Received: from localhost (141.80.246.58 [141.80.246.58]) by mx.zohomail.com with SMTPS id 1491410404499940.8845445169707; Wed, 5 Apr 2017 09:40:04 -0700 (PDT) User-agent: mu4e 0.9.18; emacs 25.1.1 From: Ricardo Wurmus To: guix-patches@gnu.org Subject: Various improvements to the CRAN importer X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 05 Apr 2017 18:40:02 +0200 Message-ID: <8737dm3j19.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -4.0 (----) The following patch series improves the CRAN importer. ------------=_1494964141-2010-1--