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Fri, 27 Jan 2023 07:13:48 -0800 (PST) References: <877cxyp1wf.fsf@gmail.com> <87y1qdo3qq.fsf@gmail.com> <87wn5rfldh.fsf_-_@gnu.org> <875ydau2vf.fsf@gmail.com> <87wn5q9epc.fsf@gnu.org> <87bkn1m4dj.fsf@gmail.com> <875yd5i5v8.fsf@gnu.org> <878rhqrzzv.fsf@gnu.org> User-agent: mu4e 1.8.13; emacs 28.2 From: =?UTF-8?Q?Tor-bj=C3=B6rn?= Claesson Date: Fri, 27 Jan 2023 17:06:37 +0200 In-reply-to: <878rhqrzzv.fsf@gnu.org> Message-ID: <878rhoxb6c.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1674832526; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post: dkim-signature; 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dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=KHNqJZ9H; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Scanner: scn0.migadu.com X-Migadu-Spam-Score: 0.23 X-Spam-Score: 0.23 X-Migadu-Queue-Id: 6C110249BA X-TUID: 0K6Vicc8OeV7 --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi! Ludovic Court=C3=A8s writes: > > The following tests FAILED: > 195 - TestStrictScanner1 (Failed) > 196 - TestStrictScanner2_1 (Failed) > 197 - TestStrictScanner2 (Failed) > 198 - TestStrictScanner2_2 (Failed) > Errors while running CTest > > Passing #:parallel-tests? #f doesn=E2=80=99t help. > > Could you take a look? The TestStrictScanner tests fail because they expect TestWriter to have run, but we disabled it. TestWriter, TestAnonymizer4, and TestPrinter1 are also reported as failing in the GDCM ctest dashboard (https://open.cdash.org/index.php?project=3DGDCM). It is strange that they passed previously in my local checkout (they fail now, some change in the toolchain?) I will try to look into this. For now, here is a patch to ignore the remaining failures, giving us an installable package, and also updated patches to add a bin output and use more system libraries. Investigating the remaining failing tests and using more system libraries feels like a fairly big, if fun, task possibly involving work on GDCM as well as this package. Should we close this bug report if we have a working package when the attached patches are applied? --=20 Mvh, Tor-bj=C3=B6rn Claesson --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-gdcm-Ignore-remaining-failing-tests.patch >From 7aaae11c7efc38222bfbf503e52cdb15bfccc33c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= Date: Fri, 27 Jan 2023 13:26:02 +0200 Subject: [PATCH 1/3] gnu: gdcm: Ignore remaining failing tests. gnu: gdcm: Ignore remaining failing tests. --- gnu/packages/bioinformatics.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8c75607a65..0fa7bb3746 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -18097,12 +18097,15 @@ (define-public gdcm #:configure-flags #~(list "-DGDCM_BUILD_TESTING=true" (string-append "-DCMAKE_CTEST_ARGUMENTS=-E;" - "'TestFileMetaInformation" - "|TestElement2" - "|TestSCUValidation" - "|TestWriter" + "'TestWriter" + "|TestStrictScanner1" + "|TestStrictScanner2" + "|TestStrictScanner2_1" + "|TestStrictScanner2_2" "|TestAnonymizer4" "|TestPrinter1" + ;; Disable tests that download data from the internet. + "|TestSCUValidation" "|TestEcho" "|TestFind'") "-DGDCM_DOCUMENTATION:BOOL=ON" -- 2.39.1 --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0002-gnu-gdcm-Add-bin-output.patch Content-Transfer-Encoding: quoted-printable >From 2bc5c46ca2fee406a7108e5d43ef66af2d392889 Mon Sep 17 00:00:00 2001 From: =3D?UTF-8?q?Tor-bj=3DC3=3DB6rn=3D20Claesson?=3D Date: Fri, 27 Jan 2023 14:43:32 +0200 Subject: [PATCH 2/3] gnu: gdcm: Add bin output. gnu: gdcm: Add bin output. --- gnu/packages/bioinformatics.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 0fa7bb3746..9a3c0f7d42 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -18084,7 +18084,7 @@ (define-public gdcm (base32 "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l")))) (build-system cmake-build-system) - (outputs '("out" "doc")) + (outputs '("out" "bin" "doc")) (arguments (list #:phases @@ -18093,7 +18093,14 @@ (define-public gdcm ;; The build spams =E2=80=98Fontconfig error: No writable cache ;; directories=E2=80=99 in a seemingly endless loop otherwise. (lambda _ - (setenv "HOME" "/tmp")))) + (setenv "HOME" "/tmp"))) + (add-after 'install 'move-files + ;; Move utilities to bin output. + (lambda _ + (mkdir-p (string-append #$output:bin "/bin")) + (rename-file + (string-append #$output "/bin") + (string-append #$output:bin "/bin"))))) #:configure-flags #~(list "-DGDCM_BUILD_TESTING=3Dtrue" (string-append "-DCMAKE_CTEST_ARGUMENTS=3D-E;" @@ -18105,9 +18112,13 @@ (define-public gdcm "|TestAnonymizer4" "|TestPrinter1" ;; Disable tests that download data from the = internet. + "|gdcmscu-echo-dicomserver" + "|gdcmscu-store-dicomserver" + "|gdcmscu-find-dicomserver" "|TestSCUValidation" "|TestEcho" "|TestFind'") + "-DGDCM_BUILD_APPLICATIONS:BOOL=3DON" "-DGDCM_DOCUMENTATION:BOOL=3DON" "-DGDCM_PDF_DOCUMENTATION:BOOL=3DOFF" (string-append "-DGDCM_INSTALL_DOC_DIR=3D" --=20 2.39.1 --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0003-gnu-gdcm-Use-more-system-libraries.patch Content-Transfer-Encoding: quoted-printable >From 467a7b614ccafa2de51a8e56a6ecf384fb6fa07b Mon Sep 17 00:00:00 2001 From: =3D?UTF-8?q?Tor-bj=3DC3=3DB6rn=3D20Claesson?=3D Date: Fri, 27 Jan 2023 17:03:36 +0200 Subject: [PATCH 3/3] gnu: gdcm: Use more system libraries. gnu: gdcm: Use more system libraries. --- gnu/packages/bioinformatics.scm | 48 ++++++++++++++++++++++++++++++--- 1 file changed, 45 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 9a3c0f7d42..77b3388f2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -18082,7 +18082,28 @@ (define-public gdcm (file-name (git-file-name name version)) (sha256 (base32 - "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l")))) + "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l")) + (modules '((guix build utils) + (ice-9 ftw))) + (snippet + '(begin + (define (unbundle? file) + (member file '("dicom3tools" + "gdcmexpat" + "gdcmutfcpp" + "gdcmuuid" + "gdcmzlib" + "getopt" + "KWStyle" + "pvrg" + "Release" + "VTK"))) + (with-directory-excursion "Utilities" + (for-each (lambda (utility) + (delete-file-recursively utility) + (substitute* "CMakeLists.txt" + (((string-append ".*/" utility "/.*")) "= "))) + (scandir "." unbundle?))))))) (build-system cmake-build-system) (outputs '("out" "bin" "doc")) (arguments @@ -18123,8 +18144,29 @@ (define-public gdcm "-DGDCM_PDF_DOCUMENTATION:BOOL=3DOFF" (string-append "-DGDCM_INSTALL_DOC_DIR=3D" #$output:doc "/share/doc/" #$name) - "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=3DOFF"))) ; TODO: need = =E2=80=98xsl-ns=E2=80=99 - (native-inputs (list doxygen graphviz)) + "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=3DOFF" ; TODO: need =E2= =80=98xsl-ns=E2=80=99 + ;; Libraries + "-DGDCM_USE_SYSTEM_EXPAT:BOOL=3DON" + "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=3DON" + "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=3DON" + "-DGDCM_USE_SYSTEM_POPPLER:BOOL=3DON" + "-DGDCM_USE_SYSTEM_UUID:BOOL=3DON" + "-DGDCM_USE_SYSTEM_ZLIB:BOOL=3DON" + ;; TODO: Unbundle these if possible. + "-DGDCM_USE_SYSTEM_CHARLS:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_JSON:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_LJPEG:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=3DOFF"))) + (inputs (list + expat + libxml2 + openssl + poppler + `(,util-linux "lib") + zlib)) + (native-inputs (list doxygen graphviz pkg-config)) (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page") (synopsis "Grassroots DICOM library") (description --=20 2.39.1 --=-=-=--