From unknown Sat Jun 21 10:38:39 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#36800 <36800@debbugs.gnu.org> To: bug#36800 <36800@debbugs.gnu.org> Subject: Status: [PATCH 11/11] gnu: Add r-depecher. Reply-To: bug#36800 <36800@debbugs.gnu.org> Date: Sat, 21 Jun 2025 17:38:39 +0000 retitle 36800 [PATCH 11/11] gnu: Add r-depecher. reassign 36800 guix-patches submitter 36800 zimoun severity 36800 normal tag 36800 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Jul 24 14:22:50 2019 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:51 +0000 Received: from localhost ([127.0.0.1]:38001 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuc-0005NE-Ch for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:50 -0400 Received: from lists.gnu.org ([209.51.188.17]:57385) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuJ-0005Lp-5J for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:32 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41160) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuH-0003JI-VI for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:31 -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,FREEMAIL_FROM, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuG-0007Ls-QE for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -0400 Received: from mail-wr1-x42e.google.com ([2a00:1450:4864:20::42e]:46471) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuG-0007Kn-JF for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: by mail-wr1-x42e.google.com with SMTP id z1so47975368wru.13 for ; Wed, 24 Jul 2019 11:22:28 -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=pgaMBeSPBUEIfWytGuX8ZLzsOG1AAzrXuronHOChjfQ=; b=arjY1DZIzQFyagrcaZBJyzZ2T2ROcRfcO6JCf37Y0fghwUjtnc7OdUi8mBBGcf8vOi ZGDuTAgOX2CvpF9UcTW284RetJLpHQ1zXiompK5fWQuW7PmuCatMG1lo9WpjywY/YV5Q EfPTDnZoyzcZkUluAxxn0SKMvzl0Aa5J0sGlMYz8KMKR83H+9HU8DFBRye5YybG6UW2G nzEUl5tfma6hqjPXAz3S6Ekb2A0nBwfOAI9ttyYtxkwh6y68FV7uB8tLmoVRNBI2Q8yb jHlocUl0Mz9XvnrHuFI6ra+sYTU9TbpNMl9LLLiq3DPfu4+f9SzX/cnACGdRTpKjZ2RE hcgw== 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=pgaMBeSPBUEIfWytGuX8ZLzsOG1AAzrXuronHOChjfQ=; b=Pwlk9A9Gu+hpb4t3Mn4826eHGjShPwrSED0X/aZVCIqSMY5jUHl3atnReblnYK+WKr VTaMic5wdkQ3Xtnxxiv4tXT2c/gSNH3+jV9i8MSeSYWwW3AGP85B965X26ZYkeTJT46t xdrgimk56G7blGSlXXhH937fT/Ciav+QtnONZcQvRM9CcJdbuuq18MZZcLiaWSHrOqT6 7WNM4PREytEV3rGT1gTXZZX2VNDmMahYtpEPWSINa9mXaDUfFC5KFzBLaB/stVo/bVZ/ R7EtXXZ91z8G3+t0poFeOG/Yd0XU6moO54uQ7/hGZc9HWtMZlx8Zudx08tV99tu2e2r2 HCjA== X-Gm-Message-State: APjAAAU1uMGMqkFXk0hGZEcKfoT41oRw8NYO9mICyBdhO1MifSsCqsQ6 WPfY5minMAVBRLzYS4LV8g/qgyvD X-Google-Smtp-Source: APXvYqzOY7O3H+91cgitdfrLSWMNn7eNp4gW4U+Wte0ELZHg89wmje+qFFkYGN0VOfFAZrqCrP8PQQ== X-Received: by 2002:adf:e444:: with SMTP id t4mr84470240wrm.262.1563992547529; Wed, 24 Jul 2019 11:22:27 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.26 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:27 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 11/11] gnu: Add r-depecher. Date: Wed, 24 Jul 2019 20:22:04 +0200 Message-Id: <20190724182204.6818-12-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:4864:20::42e X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: zimoun 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: -2.3 (--) * gnu/packages/bioconductor.scm (r-depecher): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64625aedd4..7c9a3b7417 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5013,3 +5013,47 @@ data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.") (license license:gpl2+))) + +(define-public r-depecher + (package + (name "r-depecher") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DepecheR" version)) + (sha256 + (base32 + "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) + (properties `((upstream-name . "DepecheR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beanplot" ,r-beanplot) + ("r-biocparallel" ,r-biocparallel) + ("r-dosnow" ,r-dosnow) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-mixomics" ,r-mixomics) + ("r-moments" ,r-moments) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-reshape2" ,r-reshape2) + ("r-viridis" ,r-viridis))) + (home-page + "https://bioconductor.org/packages/DepecheR") + (synopsis + "Determination of essential phenotypic elements of clusters in high-dimensional entities") + (description + "The purpose of this package is to identify traits in a dataset that can +separate groups. This is done on two levels. First, clustering is performed, +using an implementation of sparse K-means. Secondly, the generated clusters +are used to predict outcomes of groups of individuals based on their +distribution of observations in the different clusters. As certain clusters +with separating information will be identified, and these clusters are defined +by a sparse number of variables, this method can reduce the complexity of +data, to only emphasize the data that actually matters.") + (license license:expat))) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Jul 24 14:34:27 2019 Received: (at control) by debbugs.gnu.org; 24 Jul 2019 18:34:27 +0000 Received: from localhost ([127.0.0.1]:38038 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqM5r-0005nq-Aw for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:34:27 -0400 Received: from tobias.gr ([80.241.217.52]:34426) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqM5l-0005na-2U for control@debbugs.gnu.org; Wed, 24 Jul 2019 14:34:24 -0400 Received: by tobias.gr (OpenSMTPD) with ESMTP id 12602752 for ; Wed, 24 Jul 2019 18:34:18 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed; d=tobias.gr; h=from:to :date:message-id:mime-version:content-type; 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emacs 26.2 From: Ricardo Wurmus To: guix-patches@gnu.org Subject: Re: [bug#36800] [PATCH 11/11] gnu: Add r-depecher. In-reply-to: <20190724182204.6818-12-zimon.toutoune@gmail.com> 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, 24 Jul 2019 22:49:44 +0200 Message-ID: <87v9vr9mzb.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 135.84.80.216 X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: 36800@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: -2.3 (--) zimoun writes: > * gnu/packages/bioconductor.scm (r-depecher): New variable. This package cannot actually be built: --8<---------------cut here---------------start------------->8--- =E2=80=A6 if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` =3D=3D "Lin= ux" ]] ; then /usr/bin/strip --strip-debug DepecheR.so; fi /gnu/store/q19l04vd2za80mk1845pz7r8cz29qk43-bash-minimal-4.4.23/bin/bash: /= usr/bin/strip: No such file or directory make: *** [Makevars:6: strippedLib] Error 127 ERROR: compilation failed for package =E2=80=98DepecheR=E2=80=99 * removing =E2=80=98/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-= 1.0.3/site-library/DepecheR=E2=80=99 Backtrace: 4 (primitive-load "/gnu/store/f1ky8a22c7s5p053nci05a536j7=E2=80= =A6") In ice-9/eval.scm: 191:35 3 (_ #f) In srfi/srfi-1.scm: 863:16 2 (every1 # =E2=80=A6) In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/gnu= -build-system.scm: 799:28 1 (_ _) In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/uti= ls.scm: 616:6 0 (invoke _ . _) /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.= scm:616:6: In procedure invoke: Throw to key `srfi-34' with args `(#)'. builder for `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.d= rv' failed with exit code 1 build of /gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv f= ailed View build log at '/var/log/guix/drvs/mw/cdvlm6f17i81m16w131042cmvlfh5m-r-d= epecher-1.0.3.drv.bz2'. guix build: error: build of `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-= depecher-1.0.3.drv' failed --8<---------------cut here---------------end--------------->8--- I=E2=80=99ll modify the build phases to patch out this call to /usr/bin/str= ip. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Jul 25 05:55:14 2019 Received: (at 36800) by debbugs.gnu.org; 25 Jul 2019 09:55:14 +0000 Received: from localhost ([127.0.0.1]:38392 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqaSu-00033B-DE for submit@debbugs.gnu.org; Thu, 25 Jul 2019 05:55:14 -0400 Received: from mail-qt1-f193.google.com ([209.85.160.193]:45907) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqaSs-00032v-LJ for 36800@debbugs.gnu.org; Thu, 25 Jul 2019 05:55:11 -0400 Received: by mail-qt1-f193.google.com with SMTP id x22so43516642qtp.12 for <36800@debbugs.gnu.org>; Thu, 25 Jul 2019 02:55:10 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=p5s9O0hwSChRzePWiO6IhfLs3t2BUYtYnjembr1FFUM=; b=nXAwDpXQWLhBn5kuUK8q4XrYowHZe+BY3RrjLvYXSgQ+I/Fs5wlW8kkNTENoXPb8fc LAbYMZ7XNK1uQPj+sWLUDoiLgx0mUNmJbzrYXhf0z4LDPBW8G/UIT006lXL3Lk0G1SDh pgNImAvFHYbmf1xAlAW7meWAlnSEb7edloK4TNaE3bbtsz2L4moCFJQBoqjiOB9zttdv 25ZsWD3+j1eHP+eEtMbSSwvWT+f0ygB4nd2kVqWETnf6slU8roxOqffGHQmTvk4/yDX9 NZfhazJ/v92KGrFKXstMpAi81okph4vFnFYXbAfyIQEH1KcF37/CI3NP4k0JXUCAZ/Du Uk/w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=p5s9O0hwSChRzePWiO6IhfLs3t2BUYtYnjembr1FFUM=; b=lei+r/kMRxzznEx7jhDMR/VwgkHeCPy6gno52OGBH0yO9qwGJjUuGY6VsI7aiU38IF 3/zgPTp+aRCRTVXPpbZuB4n+halMoCHNHtCymJH19gJR4NupuhRXbeqayMzeI2zdSpM/ UuCisfBld79ODcYM6jhF5CwXHan4qbhflGLjsyrmFY4lLd5QEwRZNWcUwIs+p2JJFRYV x4DH02OWkFx1PIWOUS1RSzS0qEkNAfqtfysMFRCa2S4XX9TfveZbpld6j+9Fpb5dciq6 oWSYKASqxr4Rz0Hk8Vs6iuiJcEd4gBhWpQwcud3N0EwdGRIVDMB2Ytwo4dG61szQAzsF fg/w== X-Gm-Message-State: APjAAAVsQcP4FcL3ViYm+QzHqF3/wBiaYStpRmBqRIqPeSPSHGU8EHdt mZDjOpizEFoEsRug9DIEqBH7KjiBvsDcYZ7g2WLAzeKp X-Google-Smtp-Source: APXvYqwEhUdZ0RT7HDQh/D3/YIIQq0PUDi2d3pduQS+/tTtzKwYoetD0ObKcT5HWDdlyzMGkNhBfElF2qkNG7WPOwQ4= X-Received: by 2002:ac8:285c:: with SMTP id 28mr62933940qtr.186.1564048504928; Thu, 25 Jul 2019 02:55:04 -0700 (PDT) MIME-Version: 1.0 References: <20190724182204.6818-1-zimon.toutoune@gmail.com> <20190724182204.6818-12-zimon.toutoune@gmail.com> <87v9vr9mzb.fsf@elephly.net> In-Reply-To: <87v9vr9mzb.fsf@elephly.net> From: zimoun Date: Thu, 25 Jul 2019 11:54:53 +0200 Message-ID: Subject: Re: [bug#36800] [PATCH 11/11] gnu: Add r-depecher. To: Ricardo Wurmus Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36800 Cc: 36800@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: -1.0 (-) Hi Ricardo, Thank you for your quick feedback. On Wed, 24 Jul 2019 at 22:50, Ricardo Wurmus wrote: > > zimoun writes: > > > * gnu/packages/bioconductor.scm (r-depecher): New variable. > > This package cannot actually be built: Sorry for the annoyance. I missed `--pure` when I built the package. > --8<---------------cut here---------------start------------->8--- > =E2=80=A6 > if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` =3D=3D "L= inux" ]] ; then /usr/bin/strip --strip-debug DepecheR.so; fi > /gnu/store/q19l04vd2za80mk1845pz7r8cz29qk43-bash-minimal-4.4.23/bin/bash:= /usr/bin/strip: No such file or directory > make: *** [Makevars:6: strippedLib] Error 127 > ERROR: compilation failed for package =E2=80=98DepecheR=E2=80=99 > * removing =E2=80=98/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depeche= r-1.0.3/site-library/DepecheR=E2=80=99 > Backtrace: > 4 (primitive-load "/gnu/store/f1ky8a22c7s5p053nci05a536j7=E2= =80=A6") > In ice-9/eval.scm: > 191:35 3 (_ #f) > In srfi/srfi-1.scm: > 863:16 2 (every1 # =E2=80=A6) > In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/g= nu-build-system.scm: > 799:28 1 (_ _) > In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/u= tils.scm: > 616:6 0 (invoke _ . _) > > /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/util= s.scm:616:6: In procedure invoke: > Throw to key `srfi-34' with args `(#)'. > builder for `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3= .drv' failed with exit code 1 > build of /gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv= failed > View build log at '/var/log/guix/drvs/mw/cdvlm6f17i81m16w131042cmvlfh5m-r= -depecher-1.0.3.drv.bz2'. > guix build: error: build of `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-= r-depecher-1.0.3.drv' failed > --8<---------------cut here---------------end--------------->8--- > > I=E2=80=99ll modify the build phases to patch out this call to /usr/bin/s= trip. Just to understand, you mean patch the file `DepecheR/src/Makevars` to remove the absolute path `/usr/bin/strip` to simply `strip`. Right? All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Thu Jul 25 08:46:08 2019 Received: (at 36800) by debbugs.gnu.org; 25 Jul 2019 12:46:08 +0000 Received: from localhost ([127.0.0.1]:38502 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqd8I-00033U-Mg for submit@debbugs.gnu.org; Thu, 25 Jul 2019 08:46:08 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21312) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqd8E-00032h-DD for 36800@debbugs.gnu.org; Thu, 25 Jul 2019 08:46:04 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1564058751; cv=none; d=zoho.com; s=zohoarc; b=nTDoe+MOxwaxY8n84iyO362JpXAtZToAcTton8Ovgkr/21+TJ/dLlUqUP7ONYjQrl1k173yoqG5HEdGXaVcaazc6Ub/Gh22g8TJJ51X6YgKD3+fzXxzky7RN8qdbEsMB+13qwQsu7TUD/urC9XpHAnb5S+/QKm0nzn5ho75TPn0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1564058751; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=pUL5ucp/xYielp9brhiQPmgZPmZT30a496f61qjLyBs=; b=A/WT/8TpM9zoSL8Ctii7Itu64rStyVFHuHCWc1dZLFRPjHNx04jwKx5eHQq/EU2DHcsB6IESkpTMBlYm0h5uNQ6ocmLgEmOJTYUga1J7/uNx8VTC+ltET/VdkTFet1eo5iZaxdTcE6+5k0a1Hln2aIGYc5zloUMdf7n/xr1trho= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1564058751; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=3164; bh=pUL5ucp/xYielp9brhiQPmgZPmZT30a496f61qjLyBs=; b=PxFhTKg654yxuRIZIACh0b6a3Zb3lGq35GffnRlRtkNG8D6bg8KmjB485O9800kZ IZzlxRyALCY/cqwgyWIiAxX3lSACr/akrUfeoS4vXnMb9BFKEuq6rtTVmh+otIoH3PO 1qgay89vS1l6IkKAJ9R2mRSFeSYlq/sCfrZAlN2E= Received: from localhost (141.80.247.250 [141.80.247.250]) by mx.zohomail.com with SMTPS id 156405874922917.438103430059982; Thu, 25 Jul 2019 05:45:49 -0700 (PDT) References: <20190724182204.6818-1-zimon.toutoune@gmail.com> <20190724182204.6818-12-zimon.toutoune@gmail.com> <87v9vr9mzb.fsf@elephly.net> User-agent: mu4e 1.2.0; emacs 26.2 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#36800] [PATCH 11/11] gnu: Add r-depecher. In-reply-to: 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: Thu, 25 Jul 2019 14:45:46 +0200 Message-ID: <878ssm9tad.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36800 Cc: 36800@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: -1.0 (-) Hi, > On Wed, 24 Jul 2019 at 22:50, Ricardo Wurmus wrote: >> >> zimoun writes: >> >> > * gnu/packages/bioconductor.scm (r-depecher): New variable. >> >> This package cannot actually be built: > > Sorry for the annoyance. > I missed `--pure` when I built the package. You don=E2=80=99t need =E2=80=9C--pure=E2=80=9D because /usr won=E2=80=99t = be available in the build environment either way. >> --8<---------------cut here---------------start------------->8--- >> =E2=80=A6 >> if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` =3D=3D "= Linux" ]] ; then /usr/bin/strip --strip-debug DepecheR.so; fi >> /gnu/store/q19l04vd2za80mk1845pz7r8cz29qk43-bash-minimal-4.4.23/bin/bash= : /usr/bin/strip: No such file or directory >> make: *** [Makevars:6: strippedLib] Error 127 >> ERROR: compilation failed for package =E2=80=98DepecheR=E2=80=99 >> * removing =E2=80=98/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depech= er-1.0.3/site-library/DepecheR=E2=80=99 >> Backtrace: >> 4 (primitive-load "/gnu/store/f1ky8a22c7s5p053nci05a536j7=E2= =80=A6") >> In ice-9/eval.scm: >> 191:35 3 (_ #f) >> In srfi/srfi-1.scm: >> 863:16 2 (every1 # =E2=80=A6) >> In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/= gnu-build-system.scm: >> 799:28 1 (_ _) >> In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/= utils.scm: >> 616:6 0 (invoke _ . _) >> >> /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/uti= ls.scm:616:6: In procedure invoke: >> Throw to key `srfi-34' with args `(#)'. >> builder for `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.= 3.drv' failed with exit code 1 >> build of /gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.dr= v failed >> View build log at '/var/log/guix/drvs/mw/cdvlm6f17i81m16w131042cmvlfh5m-= r-depecher-1.0.3.drv.bz2'. >> guix build: error: build of `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m= -r-depecher-1.0.3.drv' failed >> --8<---------------cut here---------------end--------------->8--- >> >> I=E2=80=99ll modify the build phases to patch out this call to /usr/bin/= strip. > > Just to understand, you mean patch the file `DepecheR/src/Makevars` to > remove the absolute path `/usr/bin/strip` to simply `strip`. Right? The Makevars file contains a syntax error. Instead of joining the checks with =E2=80=9C&&=E2=80=9D they used =E2=80=9C&=E2=80=9D which is for= background execution. So instead of checking things and proceeding only if the checks passed they would attempt to execute /usr/bin/strip unconditionally. I only replaced the & with the intended &&, so now the check for /usr/bin/strip fails and it=E2=80=99s not executed, which is just fine. --=20 Ricardo From unknown Sat Jun 21 10:38:39 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 21 Mar 2020 11:24:03 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator