* [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7. @ 2022-05-20 8:41 Roel Janssen 2022-05-25 14:29 ` Maxim Cournoyer 0 siblings, 1 reply; 9+ messages in thread From: Roel Janssen @ 2022-05-20 8:41 UTC (permalink / raw) To: 55538 [-- Attachment #1: Type: text/plain, Size: 469 bytes --] Dear Guix, I'd like to update Virtuoso OSE to the latest release (see attached patch). Other than the version number and checksum bump I noticed that some JAR files made it in the build output. I tried removing them from the source tarball using a snippet, but then one needs to include a patch for various Makefile.am files and run the autogen.sh script. I thought this was simpler and clearer on what's actually achieved. Kind regards, Roel Janssen [-- Attachment #2: 0001-gnu-virtuoso-ose-Update-to-7.2.7.patch --] [-- Type: text/x-patch, Size: 2574 bytes --] From a5591def946ba8a5d9a2c5ccc3259efe9e43391c Mon Sep 17 00:00:00 2001 From: Roel Janssen <roel@gnu.org> Date: Fri, 20 May 2022 10:36:50 +0200 Subject: [PATCH] gnu: virtuoso-ose: Update to 7.2.7. * gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Remove pre-built blobs from the build output. --- gnu/packages/databases.scm | 25 ++++++++++++++++++++++--- 1 file changed, 22 insertions(+), 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index feedfe68e7..03e191bab2 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3229,14 +3229,14 @@ (define-public python-lmdb (define-public virtuoso-ose (package (name "virtuoso-ose") - (version "7.2.6") + (version "7.2.7") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/virtuoso/virtuoso/" version "/" "virtuoso-opensource-" version ".tar.gz")) (sha256 - (base32 "0ly7s7a3w2a2zhhi9rq9k2qlnzapqbbc1rcdqb3zqqpgg81krz9q")))) + (base32 "1853ln0smiilf3pni70gq6nmi9ps039cy44g6b5i9d2z1n9hnj02")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; Tests require a network connection. @@ -3255,7 +3255,26 @@ (define-public virtuoso-ose (for-each (lambda (file) (delete-file (string-append lib "/" file))) '("libvirtuoso-t.a" - "libvirtuoso-t.la")))))))) + "libvirtuoso-t.la"))))) + ;; Optional bundled Java archives are copied into the build output. + ;; This phase removes them. + (add-after 'install 'remove-static-libs + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) + (for-each (lambda (directory) + (delete-file-recursively + (string-append lib "/" directory))) + '("hibernate" + "jdbc-4.0" + "jdbc-4.1" + "jdbc-4.2" + "jdbc-4.3" + "jena" + "jena2" + "jena3" + "jena4" + "rdf4j" + "sesame")))))))) (inputs (list openssl net-tools readline zlib)) (home-page "http://vos.openlinksw.com/owiki/wiki/VOS/") -- 2.36.1 ^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7. 2022-05-20 8:41 [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7 Roel Janssen @ 2022-05-25 14:29 ` Maxim Cournoyer 2022-05-25 15:51 ` Roel Janssen 0 siblings, 1 reply; 9+ messages in thread From: Maxim Cournoyer @ 2022-05-25 14:29 UTC (permalink / raw) To: Roel Janssen; +Cc: 55538 Hi Roel, Roel Janssen <roel@gnu.org> writes: > Dear Guix, > > I'd like to update Virtuoso OSE to the latest release (see attached patch). > > Other than the version number and checksum bump I noticed that some JAR files made it in the build > output. I tried removing them from the source tarball using a snippet, but then one needs to > include a patch for various Makefile.am files and run the autogen.sh script. I thought this was > simpler and clearer on what's actually achieved. I fear in the future it would be easy to overlook the introduction of extra bundled jars in the source, that'd get installed. I feel it'd be preferable if we removed them all from a source snippet, at the cost of having to patch the build system (the extra complications you mentioned). Could you try it and send a revised patch? Thanks! Maxim ^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7. 2022-05-25 14:29 ` Maxim Cournoyer @ 2022-05-25 15:51 ` Roel Janssen 2022-05-27 10:47 ` Roel Janssen 0 siblings, 1 reply; 9+ messages in thread From: Roel Janssen @ 2022-05-25 15:51 UTC (permalink / raw) To: Maxim Cournoyer; +Cc: 55538 On Wed, 2022-05-25 at 10:29 -0400, Maxim Cournoyer wrote: > Hi Roel, > > Roel Janssen <roel@gnu.org> writes: > > > Dear Guix, > > > > I'd like to update Virtuoso OSE to the latest release (see attached patch). > > > > Other than the version number and checksum bump I noticed that some JAR files made it in the > > build > > output. I tried removing them from the source tarball using a snippet, but then one needs to > > include a patch for various Makefile.am files and run the autogen.sh script. I thought this was > > simpler and clearer on what's actually achieved. > > I fear in the future it would be easy to overlook the introduction of > extra bundled jars in the source, that'd get installed. I feel it'd be > preferable if we removed them all from a source snippet, at the cost of > having to patch the build system (the extra complications you > mentioned). > > Could you try it and send a revised patch? > Thank you for taking a look at it! To be fair, what the patches would do, would be to avoid including the directories that I remove. So removing the current pre-built binaries in a snippet will be equally error-prone. But I agree that you would preferably want to have a source tarball without pre-built binaries in it when running `guix build -S virtuoso-ose`. A naive patch leads to the build getting stuck, so I need to investigate the impact further. I'll report back when I have adapted the patch. THank you again for your time! Kind regards, Roel Janssen ^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7. 2022-05-25 15:51 ` Roel Janssen @ 2022-05-27 10:47 ` Roel Janssen 2022-05-29 12:44 ` Efraim Flashner 2022-05-31 13:44 ` [bug#55538] " Maxim Cournoyer 0 siblings, 2 replies; 9+ messages in thread From: Roel Janssen @ 2022-05-27 10:47 UTC (permalink / raw) To: Maxim Cournoyer; +Cc: 55538 [-- Attachment #1: Type: text/plain, Size: 1861 bytes --] On Wed, 2022-05-25 at 17:51 +0200, Roel Janssen wrote: > On Wed, 2022-05-25 at 10:29 -0400, Maxim Cournoyer wrote: > > Hi Roel, > > > > Roel Janssen <roel@gnu.org> writes: > > > > > Dear Guix, > > > > > > I'd like to update Virtuoso OSE to the latest release (see attached patch). > > > > > > Other than the version number and checksum bump I noticed that some JAR files made it in the > > > build > > > output. I tried removing them from the source tarball using a snippet, but then one needs to > > > include a patch for various Makefile.am files and run the autogen.sh script. I thought this > > > was > > > simpler and clearer on what's actually achieved. > > > > I fear in the future it would be easy to overlook the introduction of > > extra bundled jars in the source, that'd get installed. I feel it'd be > > preferable if we removed them all from a source snippet, at the cost of > > having to patch the build system (the extra complications you > > mentioned). > > > > Could you try it and send a revised patch? > > > > Thank you for taking a look at it! To be fair, what the patches would do, would be to avoid > including the directories that I remove. So removing the current pre-built binaries in a snippet > will be equally error-prone. > > But I agree that you would preferably want to have a source tarball without pre-built binaries in > it > when running `guix build -S virtuoso-ose`. > > A naive patch leads to the build getting stuck, so I need to investigate the impact further. > I'll report back when I have adapted the patch. > > THank you again for your time! I attached an updated patch that removes the pre-built binaries in a snippet. It then removes these directories from the build system which in turn requires one to re-run autogen.sh. Kind regards, Roel Janssen [-- Attachment #2: 0001-gnu-virtuoso-ose-Update-to-7.2.7.patch --] [-- Type: text/x-patch, Size: 7542 bytes --] From 1f3b9db55cac790711ece613f5ebeb51474764a7 Mon Sep 17 00:00:00 2001 From: Roel Janssen <roel@gnu.org> Date: Fri, 27 May 2022 12:40:46 +0200 Subject: [PATCH] gnu: virtuoso-ose: Update to 7.2.7. * gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen after applying the patch below. * gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch: New file. --- gnu/packages/databases.scm | 26 +++- ...tuoso-ose-remove-pre-built-jar-files.patch | 117 ++++++++++++++++++ 2 files changed, 141 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 2161340ef9..58b6dd088c 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -100,6 +100,7 @@ (define-module (gnu packages databases) #:use-module (gnu packages gnome) #:use-module (gnu packages gnupg) #:use-module (gnu packages golang) + #:use-module (gnu packages gperf) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages icu4c) @@ -3229,14 +3230,30 @@ (define-public python-lmdb (define-public virtuoso-ose (package (name "virtuoso-ose") - (version "7.2.6") + (version "7.2.7") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/virtuoso/virtuoso/" version "/" "virtuoso-opensource-" version ".tar.gz")) (sha256 - (base32 "0ly7s7a3w2a2zhhi9rq9k2qlnzapqbbc1rcdqb3zqqpgg81krz9q")))) + (base32 "1853ln0smiilf3pni70gq6nmi9ps039cy44g6b5i9d2z1n9hnj02")) + (patches (search-patches "virtuoso-ose-remove-pre-built-jar-files.patch")) + (modules '((guix build utils))) + ;; This snippet removes pre-built Java archives. + (snippet + '(begin + (delete-file-recursively "libsrc/JDBCDriverType4") + (delete-file-recursively "binsrc/hibernate") + (delete-file-recursively "binsrc/jena") + (delete-file-recursively "binsrc/jena2") + (delete-file-recursively "binsrc/jena3") + (delete-file-recursively "binsrc/jena4") + (delete-file-recursively "binsrc/rdf4j") + (delete-file-recursively "binsrc/sesame") + (delete-file-recursively "binsrc/sesame2") + (delete-file-recursively "binsrc/sesame3") + (delete-file-recursively "binsrc/sesame4"))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; Tests require a network connection. @@ -3247,6 +3264,9 @@ (define-public virtuoso-ose "--enable-static=no") #:phases (modify-phases %standard-phases + (add-before 'configure 'autogen + (lambda _ + (invoke "./autogen.sh"))) ;; Even with "--enable-static=no", "libvirtuoso-t.a" is left in ;; the build output. The following phase removes it. (add-after 'install 'remove-static-libs @@ -3256,6 +3276,8 @@ (define-public virtuoso-ose (delete-file (string-append lib "/" file))) '("libvirtuoso-t.a" "libvirtuoso-t.la")))))))) + (native-inputs + (list autoconf automake libtool bison flex gperf)) (inputs (list openssl net-tools readline zlib)) (home-page "http://vos.openlinksw.com/owiki/wiki/VOS/") diff --git a/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch new file mode 100644 index 0000000000..17413c71ae --- /dev/null +++ b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch @@ -0,0 +1,117 @@ +This patch disables build targets that contain pre-built Java archives that +would be copied to the build's output. + +Patch by Roel Janssen <roel@gnu.org> +*** a-virtuoso-opensource-7.2.7/binsrc/Makefile.am 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/binsrc/Makefile.am 2022-05-27 12:20:52.909135774 +0200 +*************** +*** 19,25 **** + # + # + +! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql jena jena2 jena3 jena4 sesame sesame2 sesame3 sesame4 redland hibernate dbpedia rdb2rdf rdf4j + + + # ---------------------------------------------------------------------- +--- 19,25 ---- + # + # + +! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql redland dbpedia rdb2rdf + + + # ---------------------------------------------------------------------- +*** a-virtuoso-opensource-7.2.7/configure.ac 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/configure.ac 2022-05-27 12:27:51.879208018 +0200 +*************** +*** 57,64 **** + dnl AM_INIT_AUTOMAKE([1.8]) + dnl AM_INIT_AUTOMAKE([1.9 tar-ustar]) + dnl +! AM_INIT_AUTOMAKE([1.9 tar-ustar]) +! + AM_MAINTAINER_MODE + + +--- 57,63 ---- + dnl AM_INIT_AUTOMAKE([1.8]) + dnl AM_INIT_AUTOMAKE([1.9 tar-ustar]) + dnl +! AM_INIT_AUTOMAKE([1.9 tar-ustar subdir-objects]) + AM_MAINTAINER_MODE + + +*************** +*** 3157,3163 **** + binsrc/dbpedia/Makefile + binsrc/driver/Makefile + binsrc/fct/Makefile +- binsrc/hibernate/Makefile + binsrc/hosting/Makefile + binsrc/hosting/mono/Makefile + binsrc/hosting/mono/tests/Makefile +--- 3156,3161 ---- +*************** +*** 3169,3184 **** + binsrc/hosting/ruby/Makefile + binsrc/hosting/shapefileio/Makefile + binsrc/isparql/Makefile +- binsrc/jena/Makefile +- binsrc/jena2/Makefile +- binsrc/jena3/Makefile +- binsrc/jena4/Makefile + binsrc/maildrop/Makefile + binsrc/mono/Makefile + binsrc/oat/Makefile + binsrc/rdf_mappers/Makefile + binsrc/rdb2rdf/Makefile +- binsrc/rdf4j/Makefile + binsrc/redland/Makefile + binsrc/samples/demo/Makefile + binsrc/samples/hslookup/Makefile +--- 3167,3177 ---- +*************** +*** 3191,3200 **** + binsrc/samples/webapp/Makefile + binsrc/samples/xpath/Makefile + binsrc/samples/xquery/Makefile +- binsrc/sesame/Makefile +- binsrc/sesame2/Makefile +- binsrc/sesame3/Makefile +- binsrc/sesame4/Makefile + binsrc/sqldoc/Makefile + binsrc/sync/Makefile + binsrc/tests/biftest/Makefile +--- 3184,3189 ---- +*************** +*** 3236,3245 **** + docsrc/stylesheets/Makefile + docsrc/xmlsource/Makefile + libsrc/Dk/Makefile +- libsrc/JDBCDriverType4/Makefile +- libsrc/JDBCDriverType4/testsuite_4.0/Makefile +- libsrc/JDBCDriverType4/virtuoso/jdbc/Makefile +- libsrc/JDBCDriverType4/virtuoso/Makefile + libsrc/langfunc/Makefile + libsrc/odbcsdk/Makefile + libsrc/plugin/Makefile +--- 3225,3230 ---- +*** a-virtuoso-opensource-7.2.7/libsrc/Makefile.am 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/libsrc/Makefile.am 2022-05-27 12:30:12.658593011 +0200 +*************** +*** 19,25 **** + # + # + +! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new JDBCDriverType4 + + noinst_HEADERS = Dk.h libutil.h + +--- 19,25 ---- + # + # + +! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new + + noinst_HEADERS = Dk.h libutil.h + -- 2.36.1 ^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7. 2022-05-27 10:47 ` Roel Janssen @ 2022-05-29 12:44 ` Efraim Flashner 2022-05-29 21:55 ` Roel Janssen 2022-05-31 13:44 ` [bug#55538] " Maxim Cournoyer 1 sibling, 1 reply; 9+ messages in thread From: Efraim Flashner @ 2022-05-29 12:44 UTC (permalink / raw) To: Roel Janssen; +Cc: 55538, Maxim Cournoyer [-- Attachment #1: Type: text/plain, Size: 10607 bytes --] On Fri, May 27, 2022 at 12:47:18PM +0200, Roel Janssen wrote: > On Wed, 2022-05-25 at 17:51 +0200, Roel Janssen wrote: > > On Wed, 2022-05-25 at 10:29 -0400, Maxim Cournoyer wrote: > > > Hi Roel, > > > > > > Roel Janssen <roel@gnu.org> writes: > > > > > > > Dear Guix, > > > > > > > > I'd like to update Virtuoso OSE to the latest release (see attached patch). > > > > > > > > Other than the version number and checksum bump I noticed that some JAR files made it in the > > > > build > > > > output. I tried removing them from the source tarball using a snippet, but then one needs to > > > > include a patch for various Makefile.am files and run the autogen.sh script. I thought this > > > > was > > > > simpler and clearer on what's actually achieved. > > > > > > I fear in the future it would be easy to overlook the introduction of > > > extra bundled jars in the source, that'd get installed. I feel it'd be > > > preferable if we removed them all from a source snippet, at the cost of > > > having to patch the build system (the extra complications you > > > mentioned). > > > > > > Could you try it and send a revised patch? > > > > > > > Thank you for taking a look at it! To be fair, what the patches would do, would be to avoid > > including the directories that I remove. So removing the current pre-built binaries in a snippet > > will be equally error-prone. > > > > But I agree that you would preferably want to have a source tarball without pre-built binaries in > > it > > when running `guix build -S virtuoso-ose`. > > > > A naive patch leads to the build getting stuck, so I need to investigate the impact further. > > I'll report back when I have adapted the patch. > > > > THank you again for your time! > > I attached an updated patch that removes the pre-built binaries in a snippet. It then removes these > directories from the build system which in turn requires one to re-run autogen.sh. > > Kind regards, > Roel Janssen > > From 1f3b9db55cac790711ece613f5ebeb51474764a7 Mon Sep 17 00:00:00 2001 > From: Roel Janssen <roel@gnu.org> > Date: Fri, 27 May 2022 12:40:46 +0200 > Subject: [PATCH] gnu: virtuoso-ose: Update to 7.2.7. > > * gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen > after applying the patch below. > * gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch: > New file. > --- > gnu/packages/databases.scm | 26 +++- > ...tuoso-ose-remove-pre-built-jar-files.patch | 117 ++++++++++++++++++ > 2 files changed, 141 insertions(+), 2 deletions(-) > create mode 100644 gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch > > diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm > index 2161340ef9..58b6dd088c 100644 > --- a/gnu/packages/databases.scm > +++ b/gnu/packages/databases.scm > @@ -100,6 +100,7 @@ (define-module (gnu packages databases) > #:use-module (gnu packages gnome) > #:use-module (gnu packages gnupg) > #:use-module (gnu packages golang) > + #:use-module (gnu packages gperf) > #:use-module (gnu packages gtk) > #:use-module (gnu packages guile) > #:use-module (gnu packages icu4c) > @@ -3229,14 +3230,30 @@ (define-public python-lmdb > (define-public virtuoso-ose > (package > (name "virtuoso-ose") > - (version "7.2.6") > + (version "7.2.7") > (source > (origin > (method url-fetch) > (uri (string-append "mirror://sourceforge/virtuoso/virtuoso/" version "/" > "virtuoso-opensource-" version ".tar.gz")) > (sha256 > - (base32 "0ly7s7a3w2a2zhhi9rq9k2qlnzapqbbc1rcdqb3zqqpgg81krz9q")))) > + (base32 "1853ln0smiilf3pni70gq6nmi9ps039cy44g6b5i9d2z1n9hnj02")) > + (patches (search-patches "virtuoso-ose-remove-pre-built-jar-files.patch")) > + (modules '((guix build utils))) > + ;; This snippet removes pre-built Java archives. > + (snippet > + '(begin > + (delete-file-recursively "libsrc/JDBCDriverType4") > + (delete-file-recursively "binsrc/hibernate") > + (delete-file-recursively "binsrc/jena") > + (delete-file-recursively "binsrc/jena2") > + (delete-file-recursively "binsrc/jena3") > + (delete-file-recursively "binsrc/jena4") > + (delete-file-recursively "binsrc/rdf4j") > + (delete-file-recursively "binsrc/sesame") > + (delete-file-recursively "binsrc/sesame2") > + (delete-file-recursively "binsrc/sesame3") > + (delete-file-recursively "binsrc/sesame4"))))) how about (for-each delete-file-recursively (list "libsrc/JDBCDriverType4" "binsrc/hibernate" ...)) > (build-system gnu-build-system) > (arguments > `(#:tests? #f ; Tests require a network connection. > @@ -3247,6 +3264,9 @@ (define-public virtuoso-ose > "--enable-static=no") > #:phases > (modify-phases %standard-phases > + (add-before 'configure 'autogen > + (lambda _ > + (invoke "./autogen.sh"))) This would probably be better as (replace 'bootstrap > ;; Even with "--enable-static=no", "libvirtuoso-t.a" is left in > ;; the build output. The following phase removes it. > (add-after 'install 'remove-static-libs > @@ -3256,6 +3276,8 @@ (define-public virtuoso-ose > (delete-file (string-append lib "/" file))) > '("libvirtuoso-t.a" > "libvirtuoso-t.la")))))))) > + (native-inputs > + (list autoconf automake libtool bison flex gperf)) That's more than I expected! > (inputs > (list openssl net-tools readline zlib)) > (home-page "http://vos.openlinksw.com/owiki/wiki/VOS/") > diff --git a/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch > new file mode 100644 > index 0000000000..17413c71ae > --- /dev/null > +++ b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch > @@ -0,0 +1,117 @@ > +This patch disables build targets that contain pre-built Java archives that > +would be copied to the build's output. > + > +Patch by Roel Janssen <roel@gnu.org> > +*** a-virtuoso-opensource-7.2.7/binsrc/Makefile.am 1970-01-01 01:00:01.000000000 +0100 > +--- b-virtuoso-opensource-7.2.7/binsrc/Makefile.am 2022-05-27 12:20:52.909135774 +0200 > +*************** > +*** 19,25 **** > + # > + # > + > +! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql jena jena2 jena3 jena4 sesame sesame2 sesame3 sesame4 redland hibernate dbpedia rdb2rdf rdf4j > + > + > + # ---------------------------------------------------------------------- > +--- 19,25 ---- > + # > + # > + > +! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql redland dbpedia rdb2rdf > + > + > + # ---------------------------------------------------------------------- > +*** a-virtuoso-opensource-7.2.7/configure.ac 1970-01-01 01:00:01.000000000 +0100 > +--- b-virtuoso-opensource-7.2.7/configure.ac 2022-05-27 12:27:51.879208018 +0200 > +*************** > +*** 57,64 **** > + dnl AM_INIT_AUTOMAKE([1.8]) > + dnl AM_INIT_AUTOMAKE([1.9 tar-ustar]) > + dnl > +! AM_INIT_AUTOMAKE([1.9 tar-ustar]) > +! > + AM_MAINTAINER_MODE > + > + > +--- 57,63 ---- > + dnl AM_INIT_AUTOMAKE([1.8]) > + dnl AM_INIT_AUTOMAKE([1.9 tar-ustar]) > + dnl > +! AM_INIT_AUTOMAKE([1.9 tar-ustar subdir-objects]) > + AM_MAINTAINER_MODE > + > + > +*************** > +*** 3157,3163 **** > + binsrc/dbpedia/Makefile > + binsrc/driver/Makefile > + binsrc/fct/Makefile > +- binsrc/hibernate/Makefile > + binsrc/hosting/Makefile > + binsrc/hosting/mono/Makefile > + binsrc/hosting/mono/tests/Makefile > +--- 3156,3161 ---- > +*************** > +*** 3169,3184 **** > + binsrc/hosting/ruby/Makefile > + binsrc/hosting/shapefileio/Makefile > + binsrc/isparql/Makefile > +- binsrc/jena/Makefile > +- binsrc/jena2/Makefile > +- binsrc/jena3/Makefile > +- binsrc/jena4/Makefile > + binsrc/maildrop/Makefile > + binsrc/mono/Makefile > + binsrc/oat/Makefile > + binsrc/rdf_mappers/Makefile > + binsrc/rdb2rdf/Makefile > +- binsrc/rdf4j/Makefile > + binsrc/redland/Makefile > + binsrc/samples/demo/Makefile > + binsrc/samples/hslookup/Makefile > +--- 3167,3177 ---- > +*************** > +*** 3191,3200 **** > + binsrc/samples/webapp/Makefile > + binsrc/samples/xpath/Makefile > + binsrc/samples/xquery/Makefile > +- binsrc/sesame/Makefile > +- binsrc/sesame2/Makefile > +- binsrc/sesame3/Makefile > +- binsrc/sesame4/Makefile > + binsrc/sqldoc/Makefile > + binsrc/sync/Makefile > + binsrc/tests/biftest/Makefile > +--- 3184,3189 ---- > +*************** > +*** 3236,3245 **** > + docsrc/stylesheets/Makefile > + docsrc/xmlsource/Makefile > + libsrc/Dk/Makefile > +- libsrc/JDBCDriverType4/Makefile > +- libsrc/JDBCDriverType4/testsuite_4.0/Makefile > +- libsrc/JDBCDriverType4/virtuoso/jdbc/Makefile > +- libsrc/JDBCDriverType4/virtuoso/Makefile > + libsrc/langfunc/Makefile > + libsrc/odbcsdk/Makefile > + libsrc/plugin/Makefile > +--- 3225,3230 ---- > +*** a-virtuoso-opensource-7.2.7/libsrc/Makefile.am 1970-01-01 01:00:01.000000000 +0100 > +--- b-virtuoso-opensource-7.2.7/libsrc/Makefile.am 2022-05-27 12:30:12.658593011 +0200 > +*************** > +*** 19,25 **** > + # > + # > + > +! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new JDBCDriverType4 > + > + noinst_HEADERS = Dk.h libutil.h > + > +--- 19,25 ---- > + # > + # > + > +! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new > + > + noinst_HEADERS = Dk.h libutil.h > + > -- > 2.36.1 > -- Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7. 2022-05-29 12:44 ` Efraim Flashner @ 2022-05-29 21:55 ` Roel Janssen 2022-05-30 6:21 ` Efraim Flashner 0 siblings, 1 reply; 9+ messages in thread From: Roel Janssen @ 2022-05-29 21:55 UTC (permalink / raw) To: Efraim Flashner; +Cc: 55538, Maxim Cournoyer [-- Attachment #1: Type: text/plain, Size: 4851 bytes --] Hi Efraim, Thank you for reviewing this patch. I attached a new version of the patch. I'll address your comments inline. On Sun, 2022-05-29 at 15:44 +0300, Efraim Flashner wrote: > ... > On Fri, May 27, 2022 at 12:47:18PM +0200, Roel Janssen wrote: > > From 1f3b9db55cac790711ece613f5ebeb51474764a7 Mon Sep 17 00:00:00 2001 > > From: Roel Janssen <roel@gnu.org> > > Date: Fri, 27 May 2022 12:40:46 +0200 > > Subject: [PATCH] gnu: virtuoso-ose: Update to 7.2.7. > > > > * gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen > > after applying the patch below. > > * gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch: > > New file. > > --- > > gnu/packages/databases.scm | 26 +++- > > ...tuoso-ose-remove-pre-built-jar-files.patch | 117 ++++++++++++++++++ > > 2 files changed, 141 insertions(+), 2 deletions(-) > > create mode 100644 gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch > > > > diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm > > index 2161340ef9..58b6dd088c 100644 > > --- a/gnu/packages/databases.scm > > +++ b/gnu/packages/databases.scm > > @@ -100,6 +100,7 @@ (define-module (gnu packages databases) > > #:use-module (gnu packages gnome) > > #:use-module (gnu packages gnupg) > > #:use-module (gnu packages golang) > > + #:use-module (gnu packages gperf) > > #:use-module (gnu packages gtk) > > #:use-module (gnu packages guile) > > #:use-module (gnu packages icu4c) > > @@ -3229,14 +3230,30 @@ (define-public python-lmdb > > (define-public virtuoso-ose > > (package > > (name "virtuoso-ose") > > - (version "7.2.6") > > + (version "7.2.7") > > (source > > (origin > > (method url-fetch) > > (uri (string-append "mirror://sourceforge/virtuoso/virtuoso/" version "/" > > "virtuoso-opensource-" version ".tar.gz")) > > (sha256 > > - (base32 "0ly7s7a3w2a2zhhi9rq9k2qlnzapqbbc1rcdqb3zqqpgg81krz9q")))) > > + (base32 "1853ln0smiilf3pni70gq6nmi9ps039cy44g6b5i9d2z1n9hnj02")) > > + (patches (search-patches "virtuoso-ose-remove-pre-built-jar-files.patch")) > > + (modules '((guix build utils))) > > + ;; This snippet removes pre-built Java archives. > > + (snippet > > + '(begin > > + (delete-file-recursively "libsrc/JDBCDriverType4") > > + (delete-file-recursively "binsrc/hibernate") > > + (delete-file-recursively "binsrc/jena") > > + (delete-file-recursively "binsrc/jena2") > > + (delete-file-recursively "binsrc/jena3") > > + (delete-file-recursively "binsrc/jena4") > > + (delete-file-recursively "binsrc/rdf4j") > > + (delete-file-recursively "binsrc/sesame") > > + (delete-file-recursively "binsrc/sesame2") > > + (delete-file-recursively "binsrc/sesame3") > > + (delete-file-recursively "binsrc/sesame4"))))) > > how about > (for-each delete-file-recursively > (list "libsrc/JDBCDriverType4" > "binsrc/hibernate" > ...)) > I adapted this in the new patch. > > (build-system gnu-build-system) > > (arguments > > `(#:tests? #f ; Tests require a network connection. > > @@ -3247,6 +3264,9 @@ (define-public virtuoso-ose > > "--enable-static=no") > > #:phases > > (modify-phases %standard-phases > > + (add-before 'configure 'autogen > > + (lambda _ > > + (invoke "./autogen.sh"))) > > This would probably be better as (replace 'bootstrap > I adapted this in the new patch. > > ;; Even with "--enable-static=no", "libvirtuoso-t.a" is left in > > ;; the build output. The following phase removes it. > > (add-after 'install 'remove-static-libs > > @@ -3256,6 +3276,8 @@ (define-public virtuoso-ose > > (delete-file (string-append lib "/" file))) > > '("libvirtuoso-t.a" > > "libvirtuoso-t.la")))))))) > > + (native-inputs > > + (list autoconf automake libtool bison flex gperf)) > > That's more than I expected! Yes, it's unfortunate that we apply changes to the build system code. :) Without any of these, the build fails. > > ... Kind regards, Roel Janssen [-- Attachment #2: 0001-gnu-virtuoso-ose-Update-to-7.2.7.patch --] [-- Type: text/x-patch, Size: 7429 bytes --] From c10b02ab9b962433eadc9022f77aec74cce6836c Mon Sep 17 00:00:00 2001 From: Roel Janssen <roel@gnu.org> Date: Sun, 29 May 2022 23:53:05 +0200 Subject: [PATCH] gnu: virtuoso-ose: Update to 7.2.7. * gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen after applying the patch below. * gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch: New file. --- gnu/packages/databases.scm | 26 +++- ...tuoso-ose-remove-pre-built-jar-files.patch | 117 ++++++++++++++++++ 2 files changed, 141 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 2d72c78233..e1b4fcf78e 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -100,6 +100,7 @@ (define-module (gnu packages databases) #:use-module (gnu packages gnome) #:use-module (gnu packages gnupg) #:use-module (gnu packages golang) + #:use-module (gnu packages gperf) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages icu4c) @@ -3229,14 +3230,30 @@ (define-public python-lmdb (define-public virtuoso-ose (package (name "virtuoso-ose") - (version "7.2.6") + (version "7.2.7") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/virtuoso/virtuoso/" version "/" "virtuoso-opensource-" version ".tar.gz")) (sha256 - (base32 "0ly7s7a3w2a2zhhi9rq9k2qlnzapqbbc1rcdqb3zqqpgg81krz9q")))) + (base32 "1853ln0smiilf3pni70gq6nmi9ps039cy44g6b5i9d2z1n9hnj02")) + (patches (search-patches "virtuoso-ose-remove-pre-built-jar-files.patch")) + (modules '((guix build utils))) + ;; This snippet removes pre-built Java archives. + (snippet + '(for-each delete-file-recursively + (list "binsrc/hibernate" + "binsrc/jena" + "binsrc/jena2" + "binsrc/jena3" + "binsrc/jena4" + "binsrc/rdf4j" + "binsrc/sesame" + "binsrc/sesame2" + "binsrc/sesame3" + "binsrc/sesame4" + "libsrc/JDBCDriverType4"))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; Tests require a network connection. @@ -3247,6 +3264,9 @@ (define-public virtuoso-ose "--enable-static=no") #:phases (modify-phases %standard-phases + (replace 'bootstrap + (lambda _ + (invoke "sh" "autogen.sh"))) ;; Even with "--enable-static=no", "libvirtuoso-t.a" is left in ;; the build output. The following phase removes it. (add-after 'install 'remove-static-libs @@ -3256,6 +3276,8 @@ (define-public virtuoso-ose (delete-file (string-append lib "/" file))) '("libvirtuoso-t.a" "libvirtuoso-t.la")))))))) + (native-inputs + (list autoconf automake libtool bison flex gperf)) (inputs (list openssl net-tools readline zlib)) (home-page "http://vos.openlinksw.com/owiki/wiki/VOS/") diff --git a/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch new file mode 100644 index 0000000000..17413c71ae --- /dev/null +++ b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch @@ -0,0 +1,117 @@ +This patch disables build targets that contain pre-built Java archives that +would be copied to the build's output. + +Patch by Roel Janssen <roel@gnu.org> +*** a-virtuoso-opensource-7.2.7/binsrc/Makefile.am 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/binsrc/Makefile.am 2022-05-27 12:20:52.909135774 +0200 +*************** +*** 19,25 **** + # + # + +! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql jena jena2 jena3 jena4 sesame sesame2 sesame3 sesame4 redland hibernate dbpedia rdb2rdf rdf4j + + + # ---------------------------------------------------------------------- +--- 19,25 ---- + # + # + +! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql redland dbpedia rdb2rdf + + + # ---------------------------------------------------------------------- +*** a-virtuoso-opensource-7.2.7/configure.ac 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/configure.ac 2022-05-27 12:27:51.879208018 +0200 +*************** +*** 57,64 **** + dnl AM_INIT_AUTOMAKE([1.8]) + dnl AM_INIT_AUTOMAKE([1.9 tar-ustar]) + dnl +! AM_INIT_AUTOMAKE([1.9 tar-ustar]) +! + AM_MAINTAINER_MODE + + +--- 57,63 ---- + dnl AM_INIT_AUTOMAKE([1.8]) + dnl AM_INIT_AUTOMAKE([1.9 tar-ustar]) + dnl +! AM_INIT_AUTOMAKE([1.9 tar-ustar subdir-objects]) + AM_MAINTAINER_MODE + + +*************** +*** 3157,3163 **** + binsrc/dbpedia/Makefile + binsrc/driver/Makefile + binsrc/fct/Makefile +- binsrc/hibernate/Makefile + binsrc/hosting/Makefile + binsrc/hosting/mono/Makefile + binsrc/hosting/mono/tests/Makefile +--- 3156,3161 ---- +*************** +*** 3169,3184 **** + binsrc/hosting/ruby/Makefile + binsrc/hosting/shapefileio/Makefile + binsrc/isparql/Makefile +- binsrc/jena/Makefile +- binsrc/jena2/Makefile +- binsrc/jena3/Makefile +- binsrc/jena4/Makefile + binsrc/maildrop/Makefile + binsrc/mono/Makefile + binsrc/oat/Makefile + binsrc/rdf_mappers/Makefile + binsrc/rdb2rdf/Makefile +- binsrc/rdf4j/Makefile + binsrc/redland/Makefile + binsrc/samples/demo/Makefile + binsrc/samples/hslookup/Makefile +--- 3167,3177 ---- +*************** +*** 3191,3200 **** + binsrc/samples/webapp/Makefile + binsrc/samples/xpath/Makefile + binsrc/samples/xquery/Makefile +- binsrc/sesame/Makefile +- binsrc/sesame2/Makefile +- binsrc/sesame3/Makefile +- binsrc/sesame4/Makefile + binsrc/sqldoc/Makefile + binsrc/sync/Makefile + binsrc/tests/biftest/Makefile +--- 3184,3189 ---- +*************** +*** 3236,3245 **** + docsrc/stylesheets/Makefile + docsrc/xmlsource/Makefile + libsrc/Dk/Makefile +- libsrc/JDBCDriverType4/Makefile +- libsrc/JDBCDriverType4/testsuite_4.0/Makefile +- libsrc/JDBCDriverType4/virtuoso/jdbc/Makefile +- libsrc/JDBCDriverType4/virtuoso/Makefile + libsrc/langfunc/Makefile + libsrc/odbcsdk/Makefile + libsrc/plugin/Makefile +--- 3225,3230 ---- +*** a-virtuoso-opensource-7.2.7/libsrc/Makefile.am 1970-01-01 01:00:01.000000000 +0100 +--- b-virtuoso-opensource-7.2.7/libsrc/Makefile.am 2022-05-27 12:30:12.658593011 +0200 +*************** +*** 19,25 **** + # + # + +! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new JDBCDriverType4 + + noinst_HEADERS = Dk.h libutil.h + +--- 19,25 ---- + # + # + +! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new + + noinst_HEADERS = Dk.h libutil.h + -- 2.36.1 ^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7. 2022-05-29 21:55 ` Roel Janssen @ 2022-05-30 6:21 ` Efraim Flashner 2022-05-30 7:09 ` bug#55538: " Roel Janssen 0 siblings, 1 reply; 9+ messages in thread From: Efraim Flashner @ 2022-05-30 6:21 UTC (permalink / raw) To: Roel Janssen; +Cc: 55538, Maxim Cournoyer [-- Attachment #1: Type: text/plain, Size: 291 bytes --] Go ahead and sort the native-inputs alphabetically and it looks good to me! -- Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 9+ messages in thread
* bug#55538: [PATCH] gnu: virtuoso-ose: Update to 7.2.7. 2022-05-30 6:21 ` Efraim Flashner @ 2022-05-30 7:09 ` Roel Janssen 0 siblings, 0 replies; 9+ messages in thread From: Roel Janssen @ 2022-05-30 7:09 UTC (permalink / raw) To: Efraim Flashner; +Cc: 55538-done, Maxim Cournoyer On Mon, 2022-05-30 at 09:21 +0300, Efraim Flashner wrote: > Go ahead and sort the native-inputs alphabetically and it looks good to > me! > Thanks! I ordered the native-inputs alphabetically and pushed. Kind regards, Roel Janssen ^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7. 2022-05-27 10:47 ` Roel Janssen 2022-05-29 12:44 ` Efraim Flashner @ 2022-05-31 13:44 ` Maxim Cournoyer 1 sibling, 0 replies; 9+ messages in thread From: Maxim Cournoyer @ 2022-05-31 13:44 UTC (permalink / raw) To: Roel Janssen; +Cc: 55538 Hello, Roel Janssen <roel@gnu.org> writes: > On Wed, 2022-05-25 at 17:51 +0200, Roel Janssen wrote: >> On Wed, 2022-05-25 at 10:29 -0400, Maxim Cournoyer wrote: >> > Hi Roel, >> > >> > Roel Janssen <roel@gnu.org> writes: >> > >> > > Dear Guix, >> > > >> > > I'd like to update Virtuoso OSE to the latest release (see attached patch). >> > > >> > > Other than the version number and checksum bump I noticed that some JAR files made it in the >> > > build >> > > output. I tried removing them from the source tarball using a snippet, but then one needs to >> > > include a patch for various Makefile.am files and run the autogen.sh script. I thought this >> > > was >> > > simpler and clearer on what's actually achieved. >> > >> > I fear in the future it would be easy to overlook the introduction of >> > extra bundled jars in the source, that'd get installed. I feel it'd be >> > preferable if we removed them all from a source snippet, at the cost of >> > having to patch the build system (the extra complications you >> > mentioned). >> > >> > Could you try it and send a revised patch? >> > >> >> Thank you for taking a look at it! To be fair, what the patches would do, would be to avoid >> including the directories that I remove. So removing the current pre-built binaries in a snippet >> will be equally error-prone. The way I deal with this is to have an allow list of things to preserve in the source instead of a deny list; this way if new binaries get added and need to be handled, the build will break instead of using the bundled binaries silently. Thanks for the package update (and to Efraim for picking up the review where I had left it)! Maxim ^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2022-05-31 13:46 UTC | newest] Thread overview: 9+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2022-05-20 8:41 [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7 Roel Janssen 2022-05-25 14:29 ` Maxim Cournoyer 2022-05-25 15:51 ` Roel Janssen 2022-05-27 10:47 ` Roel Janssen 2022-05-29 12:44 ` Efraim Flashner 2022-05-29 21:55 ` Roel Janssen 2022-05-30 6:21 ` Efraim Flashner 2022-05-30 7:09 ` bug#55538: " Roel Janssen 2022-05-31 13:44 ` [bug#55538] " Maxim Cournoyer
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