Bruno Victal <mirai@HIDDEN>
to control <at> debbugs.gnu.org.
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From: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN>
To: Tobias Geerinckx-Rice <me@HIDDEN>
Subject: Re: [bug#60640] Gnu: Add gdcm
Date: Wed, 11 Jan 2023 07:29:10 +0200
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Hi!
Tobias Geerinckx-Rice <me@HIDDEN> writes:
>
>> 3. It does not perform tests.
>
> OK, I'll take a look.
>
> If tests are disabled, the reason should always be noted in a comment.
> Even if it's just =E2=80=98; no test suite=E2=80=99.
>
#:tests? #t makes the build fail with "make: *** No rule to make target
'test'. Stop."
=20
GDCM has nightly regression tests
(https://open.cdash.org/index.php?project=3DGDCM), should we try to run
those when building? I have tried to find out how to do this but for now
with no success. Maybe it is obvious to more experienced people?
>> +(define-public gdcm
>
> It used to be common to unconditionally add packages to the end of
> files, but this needlessly increased the risk of merge conflicts.
>
> Instead, just add them wherever they first fit alphabetically; here, I
> put it above =E2=80=98mia=E2=80=99.
>
Ok, will do from now on!
>> + (version "3.0.20")
>
> =E2=80=98guix lint=E2=80=99 says this can be updated to 3.1.0 but I didn'=
t try, as I'd
> rather it be tested by an actual user =E2=80=94 i.e., you.
>
I got that too, but the latest release in git is 3.0.20
>> + "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))))
>> + (build-system cmake-build-system)
>> + (outputs '("out" "doc"))
>
> /share/doc wasn't actually installed into "doc", but to "out", so I
> set the GDCM_INSTALL_DOC_DIR configure flag.
>
>> + (arguments
>> + (list #:tests? #f
>> + #:phases #~(modify-phases %standard-phases
>> + (add-before 'configure 'set-LDFLAGS
>> + (lambda* (#:key inputs outputs
>> #:allow-other-keys)
>> + (setenv "LDFLAGS"
>> + (string-append "-Wl,-rpath=3D"
>> + #$output
>> "/lib"))))
>> + (add-before 'build 'patch-gdcm-charls.h
>> + (lambda _
>> + (substitute*
>> "../source/Utilities/gdcm_charls.h"
>> + (("# include <CharLS/charls.h>")
Ah, good catch!
>
> Purely as a matter of taste I dropped the =E2=80=98# include =E2=80=99 fr=
om both
> strings and escaped the =E2=80=98.=E2=80=99 in the regexp.
>
>> + "# include <charls/charls.h>"))
>> #t)))
>
> =E2=80=98#t=E2=80=99 endings are also obsolete. Just drop them entirely.=
Phases can
> now safely return anything, including nothing or undefined.
>
> I added the following phase to work around log spam, since I didn't
> find its source (nor did I look very hard) [edit: it was indeed
> graphviz, thanks]. By default, $HOME is not writable in the build
> environment.
>
> (add-before 'build 'set-HOME
> ;; The build spams =E2=80=98Fontconfig error: No writable cache
> ;; directories=E2=80=99 in a seemingly endless loop otherwise.
> (lambda _
> (setenv "HOME" "/tmp")))
>
>> + #:configure-flags #~(list "-DCMAKE_SKIP_RPATH:BOOL=3DYES"
Is this needed, btw? It came from gdcm:s packaging
instructions. Removing it causes no verify-runpath issues.
>
> I, opinionated, added newlines after #:phases and #:configure-flags.
>
> Some people like the =E2=80=98extreme indentation=E2=80=99 you get by thr=
owing away
> half of your screen width. I find it leads to cramped code and noisy
> patches once the phases need to get actual work done or an even longer
> CMAKE_ flag comes along.
>
> I also added some newlines and tried to group related flags.
>
Thanks, I didn't know that would make the line fit better on
screen. Much neater=3D)
>> + "-DCMAKE_C_FLAGS=3D-fvisibility=3Dhidden"
>> + "-DCMAKE_CXX_FLAGS=3D-fvisibility=3Dhidden"
>
> Should these be explained in a very brief comment?
>
They are from https://github.com/malaterre/GDCM/blob/master/PACKAGER,
the explanation is:
"This make sure that on UNIX, the API is actually identical at what is foun=
d on Windows."
>
> Thank you for building with system libraries! Also remove the bundled
> copies when possible. I did so in a (rather strict) source snippet.
>
Ok, neat=3D)
>> + "-DGDCM_PDF_DOCUMENTATION:BOOL=3DOFF"
>
> I cannot get the man pages to build, either. They need something
> called =E2=80=98xsl-ns=E2=80=99. I've disabled GDCM_BUILD_DOCBOOK_MANPAG=
ES for now.
>
>> + "-DGCM_BUILD_TESTING:BOOL=3DOFF"
>
> Why is this set? It's reported by CMake as having no effect, and a
> diff of the output confirms that.
>
From the old wiki:
"This boolean is responsible for deciding whether or not to build/run the
nightly regression test of gdcm. Warning when turning this option on,
the size of the gdcm libraries will be bigger since some extra code are
compiled in for the testing framework (see gdcm::Testing, and the md5
lib)."
This seems to be incorrect then, maybe we can skip it.
>> + (license license:bsd-3)))
>
> I still need to check this.
>
https://github.com/malaterre/GDCM/blob/master/Copyright.txt
I'm not able to apply your new patch, but that is probably a fault on my pa=
rt.
Thanks a lot for sharing your time and knowledge, and for making this
patch neater! I find this a lot of fun, but have no experience
with scheme or packaging, so your explanations are very valuable to me.
Cheers
Tor-bj=C3=B6rn
guix-patches@HIDDEN:bug#60640; Package guix-patches.
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From: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN>
To: Tobias Geerinckx-Rice <me@HIDDEN>
Subject: Re: [bug#60640] Gnu: Add gdcm
Date: Wed, 11 Jan 2023 07:29:10 +0200
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Hi!
Tobias Geerinckx-Rice <me@HIDDEN> writes:
>
>> 3. It does not perform tests.
>
> OK, I'll take a look.
>
> If tests are disabled, the reason should always be noted in a comment.
> Even if it's just =E2=80=98; no test suite=E2=80=99.
>
#:tests? #t makes the build fail with "make: *** No rule to make target
'test'. Stop."
=20
GDCM has nightly regression tests
(https://open.cdash.org/index.php?project=3DGDCM), should we try to run
those when building? I have tried to find out how to do this but for now
with no success. Maybe it is obvious to more experienced people?
>> +(define-public gdcm
>
> It used to be common to unconditionally add packages to the end of
> files, but this needlessly increased the risk of merge conflicts.
>
> Instead, just add them wherever they first fit alphabetically; here, I
> put it above =E2=80=98mia=E2=80=99.
>
Ok, will do from now on!
>> + (version "3.0.20")
>
> =E2=80=98guix lint=E2=80=99 says this can be updated to 3.1.0 but I didn'=
t try, as I'd
> rather it be tested by an actual user =E2=80=94 i.e., you.
>
I got that too, but the latest release in git is 3.0.20
>> + "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))))
>> + (build-system cmake-build-system)
>> + (outputs '("out" "doc"))
>
> /share/doc wasn't actually installed into "doc", but to "out", so I
> set the GDCM_INSTALL_DOC_DIR configure flag.
>
>> + (arguments
>> + (list #:tests? #f
>> + #:phases #~(modify-phases %standard-phases
>> + (add-before 'configure 'set-LDFLAGS
>> + (lambda* (#:key inputs outputs
>> #:allow-other-keys)
>> + (setenv "LDFLAGS"
>> + (string-append "-Wl,-rpath=3D"
>> + #$output
>> "/lib"))))
>> + (add-before 'build 'patch-gdcm-charls.h
>> + (lambda _
>> + (substitute*
>> "../source/Utilities/gdcm_charls.h"
>> + (("# include <CharLS/charls.h>")
Ah, good catch!
>
> Purely as a matter of taste I dropped the =E2=80=98# include =E2=80=99 fr=
om both
> strings and escaped the =E2=80=98.=E2=80=99 in the regexp.
>
>> + "# include <charls/charls.h>"))
>> #t)))
>
> =E2=80=98#t=E2=80=99 endings are also obsolete. Just drop them entirely.=
Phases can
> now safely return anything, including nothing or undefined.
>
> I added the following phase to work around log spam, since I didn't
> find its source (nor did I look very hard) [edit: it was indeed
> graphviz, thanks]. By default, $HOME is not writable in the build
> environment.
>
> (add-before 'build 'set-HOME
> ;; The build spams =E2=80=98Fontconfig error: No writable cache
> ;; directories=E2=80=99 in a seemingly endless loop otherwise.
> (lambda _
> (setenv "HOME" "/tmp")))
>
>> + #:configure-flags #~(list "-DCMAKE_SKIP_RPATH:BOOL=3DYES"
Is this needed, btw? It came from gdcm:s packaging
instructions. Removing it causes no verify-runpath issues.
>
> I, opinionated, added newlines after #:phases and #:configure-flags.
>
> Some people like the =E2=80=98extreme indentation=E2=80=99 you get by thr=
owing away
> half of your screen width. I find it leads to cramped code and noisy
> patches once the phases need to get actual work done or an even longer
> CMAKE_ flag comes along.
>
> I also added some newlines and tried to group related flags.
>
Thanks, I didn't know that would make the line fit better on
screen. Much neater=3D)
>> + "-DCMAKE_C_FLAGS=3D-fvisibility=3Dhidden"
>> + "-DCMAKE_CXX_FLAGS=3D-fvisibility=3Dhidden"
>
> Should these be explained in a very brief comment?
>
They are from https://github.com/malaterre/GDCM/blob/master/PACKAGER,
the explanation is:
"This make sure that on UNIX, the API is actually identical at what is foun=
d on Windows."
>
> Thank you for building with system libraries! Also remove the bundled
> copies when possible. I did so in a (rather strict) source snippet.
>
Ok, neat=3D)
>> + "-DGDCM_PDF_DOCUMENTATION:BOOL=3DOFF"
>
> I cannot get the man pages to build, either. They need something
> called =E2=80=98xsl-ns=E2=80=99. I've disabled GDCM_BUILD_DOCBOOK_MANPAG=
ES for now.
>
>> + "-DGCM_BUILD_TESTING:BOOL=3DOFF"
>
> Why is this set? It's reported by CMake as having no effect, and a
> diff of the output confirms that.
>
From the old wiki:
"This boolean is responsible for deciding whether or not to build/run the
nightly regression test of gdcm. Warning when turning this option on,
the size of the gdcm libraries will be bigger since some extra code are
compiled in for the testing framework (see gdcm::Testing, and the md5
lib)."
This seems to be incorrect then, maybe we can skip it.
>> + (license license:bsd-3)))
>
> I still need to check this.
>
https://github.com/malaterre/GDCM/blob/master/Copyright.txt
I'm not able to apply your new patch, but that is probably a fault on my pa=
rt.
Thanks a lot for sharing your time and knowledge, and for making this
patch neater! I find this a lot of fun, but have no experience
with scheme or packaging, so your explanations are very valuable to me.
Cheers
Tor-bj=C3=B6rn
guix-patches@HIDDEN:bug#60640; Package guix-patches.
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References: <877cxyp1wf.fsf@HIDDEN>
From: Tobias Geerinckx-Rice <me@HIDDEN>
To: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN>
Subject: Re: [bug#60640] Gnu: Add gdcm
Date: Tue, 10 Jan 2023 15:52:49 +0100
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Content preview: Tor-björn Claesson 写道： > 1. I have not yet been able
to build the bin output, > which consists of utilities for manipulating DICOM
data. OK, I'll take a look. > 2. It does not build pdf-documentation, since
that would require > texlive as a native input.
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Tor-bj=C3=B6rn Claesson =E5=86=99=E9=81=93=EF=BC=9A
> 1. I have not yet been able to build the bin output,
> which consists of utilities for manipulating DICOM data.=20
OK, I'll take a look.
> 2. It does not build pdf-documentation, since that would require
> texlive as a native input.
OK. You can add this sort of information as a comment by the=20
relevant line, so it doesn't get lost (even during review :-).
> 3. It does not perform tests.
OK, I'll take a look.
If tests are disabled, the reason should always be noted in a=20
comment. Even if it's just =E2=80=98; no test suite=E2=80=99.
> 4. It uses socketxx, ljpeg and papyrus3 from the gdcm sources.
Here too I've punted on that by just adding a comment for now.
> +(define-public gdcm
It used to be common to unconditionally add packages to the end of=20
files, but this needlessly increased the risk of merge conflicts.
Instead, just add them wherever they first fit alphabetically;=20
here, I put it above =E2=80=98mia=E2=80=99.
> + (version "3.0.20")
=E2=80=98guix lint=E2=80=99 says this can be updated to 3.1.0 but I didn't =
try, as=20
I'd rather it be tested by an actual user =E2=80=94 i.e., you.
> +=20
> "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))))
> + (build-system cmake-build-system)
> + (outputs '("out" "doc"))
/share/doc wasn't actually installed into "doc", but to "out", so=20
I set the GDCM_INSTALL_DOC_DIR configure flag.
> + (arguments
> + (list #:tests? #f
> + #:phases #~(modify-phases %standard-phases
> + (add-before 'configure 'set-LDFLAGS
> + (lambda* (#:key inputs outputs=20
> #:allow-other-keys)
> + (setenv "LDFLAGS"
> + (string-append=20
> "-Wl,-rpath=3D"
> + #$output=20
> "/lib"))))
> + (add-before 'build 'patch-gdcm-charls.h
> + (lambda _
> + (substitute*=20
> "../source/Utilities/gdcm_charls.h"
> + (("# include <CharLS/charls.h>")
Purely as a matter of taste I dropped the =E2=80=98# include =E2=80=99 from=
both=20
strings and escaped the =E2=80=98.=E2=80=99 in the regexp.
> + "# include <charls/charls.h>"))=20
> #t)))
=E2=80=98#t=E2=80=99 endings are also obsolete. Just drop them entirely. =
Phases=20
can now safely return anything, including nothing or undefined.
I added the following phase to work around log spam, since I=20
didn't find its source (nor did I look very hard) [edit: it was=20
indeed graphviz, thanks]. By default, $HOME is not writable in=20
the build environment.
(add-before 'build 'set-HOME
;; The build spams =E2=80=98Fontconfig error: No writable cache
;; directories=E2=80=99 in a seemingly endless loop otherwise.
(lambda _
(setenv "HOME" "/tmp")))
> + #:configure-flags #~(list=20
> "-DCMAKE_SKIP_RPATH:BOOL=3DYES"
I, opinionated, added newlines after #:phases and=20
#:configure-flags.
Some people like the =E2=80=98extreme indentation=E2=80=99 you get by throw=
ing=20
away half of your screen width. I find it leads to cramped code=20
and noisy patches once the phases need to get actual work done or=20
an even longer CMAKE_ flag comes along.
I also added some newlines and tried to group related flags.
> +=20
> "-DCMAKE_C_FLAGS=3D-fvisibility=3Dhidden"
> +=20
> "-DCMAKE_CXX_FLAGS=3D-fvisibility=3Dhidden"
Should these be explained in a very brief comment?
> +=20
> "-DGDCM_USE_SYSTEM_EXPAT:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_ZLIB:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_CHARLS:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_POPPLER:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_JSON:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_UUID:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=3DON"
Thank you for building with system libraries! Also remove the=20
bundled copies when possible. I did so in a (rather strict)=20
source snippet.
> +=20
> "-DGDCM_PDF_DOCUMENTATION:BOOL=3DOFF"
I cannot get the man pages to build, either. They need something=20
called =E2=80=98xsl-ns=E2=80=99. I've disabled GDCM_BUILD_DOCBOOK_MANPAGES=
for=20
now.
> +=20
> "-DGCM_BUILD_TESTING:BOOL=3DOFF"
Why is this set? It's reported by CMake as having no effect, and=20
a diff of the output confirms that.
> +=20
> "-DGDCM_BUILD_APPLICATIONS:BOOL=3DOFF"
I added a =E2=80=98TODO=E2=80=99 comment above these bundled projects:
> +=20
> "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=3DOFF"
> +=20
> "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=3DOFF"
> +=20
> "-DGDCM_USE_SYSTEM_LJPEG:BOOL=3DOFF")))
> + (inputs (list openssl
> + expat
> + charls
> + poppler
> + libxml2
> + json-c
> + openjpeg
> + `(,util-linux "lib")
> + zlib))
> + (native-inputs (list git pkg-config doxygen graphviz))
Sorted both.
> + (home-page "https://gdcm.sourceforge.net")
> + (synopsis
> + "C++ library dedicated to reading/parsing and writing=20
> DICOM medical files")
> + (description
> + "Grassroots DICOM (GDCM) is an implementation of the DICOM=20
> standard
> +designed to be open source so that researchers may access=20
> clinical data
> +directly. GDCM includes a file format definition and a network=20
> communications
> +protocol, both of which should be extended to provide a full=20
> set of tools for
> +a researcher or small medical imaging vendor to interface with=20
> an existing
> +medical database.")
I rewrote this just a smidge. Mostly to remove the extra words,=20
and use pretty @acronym{} mark-up.
> + (license license:bsd-3)))
I still need to check this.
I've attached my WIP V2 to this message, with a commit message=20
matching our conventions.
Kind regards,
T G-R
--=-=-=
Content-Type: text/x-patch; charset=utf-8
Content-Disposition: inline; filename=v2-0001-gnu-Add-gdcm.patch
Content-Transfer-Encoding: quoted-printable
From=20e2e2d9e220158aa2fd7dd0f4995c76d7d09ae79b Mon Sep 17 00:00:00 2001
From: =3D?UTF-8?q?Tor-bj=3DC3=3DB6rn=3D20Claesson?=3D <tclaesson@HIDDEN>
Date: Sat, 7 Jan 2023 21:40:42 +0200
Subject: [PATCH v2] gnu: Add gdcm.
* gnu/packages/image-processing.scm (gdcm): New variable.
Signed-off-by: Tobias Geerinckx-Rice <me@HIDDEN>
=2D--
gnu/packages/image-processing.scm | 105 ++++++++++++++++++++++++++++++
1 file changed, 105 insertions(+)
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-process=
ing.scm
index 70c820e76b..b95cb54964 100644
=2D-- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -99,6 +99,7 @@ (define-module (gnu packages image-processing)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
#:use-module (gnu packages video)
+ #:use-module (gnu packages web)
#:use-module (gnu packages xiph)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@@ -196,6 +197,110 @@ (define-public dcmtk
"A union of the Apache 2.0 licence and various non-copyleft
licences similar to the Modified BSD licence."))))
=20
+(define-public gdcm
+ (package
+ (name "gdcm")
+ (version "3.0.20")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/malaterre/GDCM/")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))
+ (modules '((guix build utils)
+ (ice-9 ftw)))
+ (snippet
+ '(begin
+ (define (unbundle? file)
+ (and (file-is-directory? file)
+ ;; Not all directories represent a bundled projec=
t,
+ ;; and some projects can't yet be unbundled.
+ (not (member file '("." ".."
+ "doxygen"
+ "gdcmext"
+ "gdcmjpeg" ; TODO
+ "gdcmrle"
+ "socketxx"))))) ; TODO
+ (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" "doc"))
+ (arguments
+ (list #:tests? #f ; XXX
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'configure 'set-LDFLAGS
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "LDFLAGS"
+ (string-append "-Wl,-rpath=3D"
+ #$output "/lib"))))
+ (add-before 'build 'set-HOME
+ ;; The build spams =E2=80=98Fontconfig error: No writable=
cache
+ ;; directories=E2=80=99 in a seemingly endless loop other=
wise.
+ (lambda _
+ (setenv "HOME" "/tmp")))
+ (add-before 'build 'patch-gdcm-charls.h
+ (lambda _
+ (substitute* "../source/Utilities/gdcm_charls.h"
+ (("<CharLS/charls\\.h>")
+ "<charls/charls.h>")))))
+ #:configure-flags
+ #~(list "-DCMAKE_SKIP_RPATH:BOOL=3DYES"
+ "-DCMAKE_BUILD_TYPE:STRING=3DRelease"
+ "-DCMAKE_C_FLAGS=3D-fvisibility=3Dhidden"
+ "-DCMAKE_CXX_FLAGS=3D-fvisibility=3Dhidden"
+ "-DGDCM_BUILD_SHARED_LIBS:BOOL=3DON"
+
+ "-DGDCM_DOCUMENTATION:BOOL=3DON"
+ "-DGDCM_PDF_DOCUMENTATION:BOOL=3DOFF" ; TODO? need texl=
ive
+ (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
+
+ "-DGDCM_USE_SYSTEM_EXPAT:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_ZLIB:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_CHARLS:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_POPPLER:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_JSON:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_UUID:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=3DON"
+
+ "-DGDCM_BUILD_APPLICATIONS:BOOL=3DOFF"
+
+ ;; TODO: Unbundle these if possible.
+ "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=3DOFF"
+ "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=3DOFF" ; socketxx in s=
nippet
+ "-DGDCM_USE_SYSTEM_LJPEG:BOOL=3DOFF"))) ; gdcmjpeg in s=
nippet
+ (inputs (list charls
+ expat
+ json-c
+ libxml2
+ openjpeg
+ openssl
+ poppler
+ `(,util-linux "lib")
+ zlib))
+ (native-inputs (list doxygen git graphviz pkg-config))
+ (home-page "https://gdcm.sourceforge.net")
+ (synopsis "C++ library to read, parse, and write DICOM medical files")
+ (description
+ "@acronym{GDCM, Grassroots DICOM} implements the @acronym{DICOM, Digi=
tal
+Imaging and Communications in Medicine} standard to let researchers access
+clinical data directly. GDCM includes a file format definition and a netw=
ork
+communications protocol, both of which should be extended to provide a ful=
l set
+of tools for a researcher or small medical imaging vendor to interface wit=
h an
+existing medical database.")
+ (license license:bsd-3)))
+
(define-public mia
(package
(name "mia")
base-commit: e0ed305f2f096e7048af1a117c72895433f4886a
=2D-=20
2.38.1
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References: <877cxyp1wf.fsf@HIDDEN>
From: Tobias Geerinckx-Rice <me@HIDDEN>
To: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN>
Subject: Re: [bug#60640] Gnu: Add gdcm
Date: Tue, 10 Jan 2023 15:52:49 +0100
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Tor-bj=C3=B6rn Claesson =E5=86=99=E9=81=93=EF=BC=9A
> 1. I have not yet been able to build the bin output,
> which consists of utilities for manipulating DICOM data.=20
OK, I'll take a look.
> 2. It does not build pdf-documentation, since that would require
> texlive as a native input.
OK. You can add this sort of information as a comment by the=20
relevant line, so it doesn't get lost (even during review :-).
> 3. It does not perform tests.
OK, I'll take a look.
If tests are disabled, the reason should always be noted in a=20
comment. Even if it's just =E2=80=98; no test suite=E2=80=99.
> 4. It uses socketxx, ljpeg and papyrus3 from the gdcm sources.
Here too I've punted on that by just adding a comment for now.
> +(define-public gdcm
It used to be common to unconditionally add packages to the end of=20
files, but this needlessly increased the risk of merge conflicts.
Instead, just add them wherever they first fit alphabetically;=20
here, I put it above =E2=80=98mia=E2=80=99.
> + (version "3.0.20")
=E2=80=98guix lint=E2=80=99 says this can be updated to 3.1.0 but I didn't =
try, as=20
I'd rather it be tested by an actual user =E2=80=94 i.e., you.
> +=20
> "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))))
> + (build-system cmake-build-system)
> + (outputs '("out" "doc"))
/share/doc wasn't actually installed into "doc", but to "out", so=20
I set the GDCM_INSTALL_DOC_DIR configure flag.
> + (arguments
> + (list #:tests? #f
> + #:phases #~(modify-phases %standard-phases
> + (add-before 'configure 'set-LDFLAGS
> + (lambda* (#:key inputs outputs=20
> #:allow-other-keys)
> + (setenv "LDFLAGS"
> + (string-append=20
> "-Wl,-rpath=3D"
> + #$output=20
> "/lib"))))
> + (add-before 'build 'patch-gdcm-charls.h
> + (lambda _
> + (substitute*=20
> "../source/Utilities/gdcm_charls.h"
> + (("# include <CharLS/charls.h>")
Purely as a matter of taste I dropped the =E2=80=98# include =E2=80=99 from=
both=20
strings and escaped the =E2=80=98.=E2=80=99 in the regexp.
> + "# include <charls/charls.h>"))=20
> #t)))
=E2=80=98#t=E2=80=99 endings are also obsolete. Just drop them entirely. =
Phases=20
can now safely return anything, including nothing or undefined.
I added the following phase to work around log spam, since I=20
didn't find its source (nor did I look very hard) [edit: it was=20
indeed graphviz, thanks]. By default, $HOME is not writable in=20
the build environment.
(add-before 'build 'set-HOME
;; The build spams =E2=80=98Fontconfig error: No writable cache
;; directories=E2=80=99 in a seemingly endless loop otherwise.
(lambda _
(setenv "HOME" "/tmp")))
> + #:configure-flags #~(list=20
> "-DCMAKE_SKIP_RPATH:BOOL=3DYES"
I, opinionated, added newlines after #:phases and=20
#:configure-flags.
Some people like the =E2=80=98extreme indentation=E2=80=99 you get by throw=
ing=20
away half of your screen width. I find it leads to cramped code=20
and noisy patches once the phases need to get actual work done or=20
an even longer CMAKE_ flag comes along.
I also added some newlines and tried to group related flags.
> +=20
> "-DCMAKE_C_FLAGS=3D-fvisibility=3Dhidden"
> +=20
> "-DCMAKE_CXX_FLAGS=3D-fvisibility=3Dhidden"
Should these be explained in a very brief comment?
> +=20
> "-DGDCM_USE_SYSTEM_EXPAT:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_ZLIB:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_CHARLS:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_POPPLER:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_JSON:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_UUID:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=3DON"
> +=20
> "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=3DON"
Thank you for building with system libraries! Also remove the=20
bundled copies when possible. I did so in a (rather strict)=20
source snippet.
> +=20
> "-DGDCM_PDF_DOCUMENTATION:BOOL=3DOFF"
I cannot get the man pages to build, either. They need something=20
called =E2=80=98xsl-ns=E2=80=99. I've disabled GDCM_BUILD_DOCBOOK_MANPAGES=
for=20
now.
> +=20
> "-DGCM_BUILD_TESTING:BOOL=3DOFF"
Why is this set? It's reported by CMake as having no effect, and=20
a diff of the output confirms that.
> +=20
> "-DGDCM_BUILD_APPLICATIONS:BOOL=3DOFF"
I added a =E2=80=98TODO=E2=80=99 comment above these bundled projects:
> +=20
> "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=3DOFF"
> +=20
> "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=3DOFF"
> +=20
> "-DGDCM_USE_SYSTEM_LJPEG:BOOL=3DOFF")))
> + (inputs (list openssl
> + expat
> + charls
> + poppler
> + libxml2
> + json-c
> + openjpeg
> + `(,util-linux "lib")
> + zlib))
> + (native-inputs (list git pkg-config doxygen graphviz))
Sorted both.
> + (home-page "https://gdcm.sourceforge.net")
> + (synopsis
> + "C++ library dedicated to reading/parsing and writing=20
> DICOM medical files")
> + (description
> + "Grassroots DICOM (GDCM) is an implementation of the DICOM=20
> standard
> +designed to be open source so that researchers may access=20
> clinical data
> +directly. GDCM includes a file format definition and a network=20
> communications
> +protocol, both of which should be extended to provide a full=20
> set of tools for
> +a researcher or small medical imaging vendor to interface with=20
> an existing
> +medical database.")
I rewrote this just a smidge. Mostly to remove the extra words,=20
and use pretty @acronym{} mark-up.
> + (license license:bsd-3)))
I still need to check this.
I've attached my WIP V2 to this message, with a commit message=20
matching our conventions.
Kind regards,
T G-R
--=-=-=
Content-Type: text/x-patch; charset=utf-8
Content-Disposition: inline; filename=v2-0001-gnu-Add-gdcm.patch
Content-Transfer-Encoding: quoted-printable
From=20e2e2d9e220158aa2fd7dd0f4995c76d7d09ae79b Mon Sep 17 00:00:00 2001
From: =3D?UTF-8?q?Tor-bj=3DC3=3DB6rn=3D20Claesson?=3D <tclaesson@HIDDEN>
Date: Sat, 7 Jan 2023 21:40:42 +0200
Subject: [PATCH v2] gnu: Add gdcm.
* gnu/packages/image-processing.scm (gdcm): New variable.
Signed-off-by: Tobias Geerinckx-Rice <me@HIDDEN>
=2D--
gnu/packages/image-processing.scm | 105 ++++++++++++++++++++++++++++++
1 file changed, 105 insertions(+)
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-process=
ing.scm
index 70c820e76b..b95cb54964 100644
=2D-- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -99,6 +99,7 @@ (define-module (gnu packages image-processing)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
#:use-module (gnu packages video)
+ #:use-module (gnu packages web)
#:use-module (gnu packages xiph)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@@ -196,6 +197,110 @@ (define-public dcmtk
"A union of the Apache 2.0 licence and various non-copyleft
licences similar to the Modified BSD licence."))))
=20
+(define-public gdcm
+ (package
+ (name "gdcm")
+ (version "3.0.20")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/malaterre/GDCM/")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))
+ (modules '((guix build utils)
+ (ice-9 ftw)))
+ (snippet
+ '(begin
+ (define (unbundle? file)
+ (and (file-is-directory? file)
+ ;; Not all directories represent a bundled projec=
t,
+ ;; and some projects can't yet be unbundled.
+ (not (member file '("." ".."
+ "doxygen"
+ "gdcmext"
+ "gdcmjpeg" ; TODO
+ "gdcmrle"
+ "socketxx"))))) ; TODO
+ (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" "doc"))
+ (arguments
+ (list #:tests? #f ; XXX
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'configure 'set-LDFLAGS
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "LDFLAGS"
+ (string-append "-Wl,-rpath=3D"
+ #$output "/lib"))))
+ (add-before 'build 'set-HOME
+ ;; The build spams =E2=80=98Fontconfig error: No writable=
cache
+ ;; directories=E2=80=99 in a seemingly endless loop other=
wise.
+ (lambda _
+ (setenv "HOME" "/tmp")))
+ (add-before 'build 'patch-gdcm-charls.h
+ (lambda _
+ (substitute* "../source/Utilities/gdcm_charls.h"
+ (("<CharLS/charls\\.h>")
+ "<charls/charls.h>")))))
+ #:configure-flags
+ #~(list "-DCMAKE_SKIP_RPATH:BOOL=3DYES"
+ "-DCMAKE_BUILD_TYPE:STRING=3DRelease"
+ "-DCMAKE_C_FLAGS=3D-fvisibility=3Dhidden"
+ "-DCMAKE_CXX_FLAGS=3D-fvisibility=3Dhidden"
+ "-DGDCM_BUILD_SHARED_LIBS:BOOL=3DON"
+
+ "-DGDCM_DOCUMENTATION:BOOL=3DON"
+ "-DGDCM_PDF_DOCUMENTATION:BOOL=3DOFF" ; TODO? need texl=
ive
+ (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
+
+ "-DGDCM_USE_SYSTEM_EXPAT:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_ZLIB:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_CHARLS:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_POPPLER:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_JSON:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_UUID:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=3DON"
+ "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=3DON"
+
+ "-DGDCM_BUILD_APPLICATIONS:BOOL=3DOFF"
+
+ ;; TODO: Unbundle these if possible.
+ "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=3DOFF"
+ "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=3DOFF" ; socketxx in s=
nippet
+ "-DGDCM_USE_SYSTEM_LJPEG:BOOL=3DOFF"))) ; gdcmjpeg in s=
nippet
+ (inputs (list charls
+ expat
+ json-c
+ libxml2
+ openjpeg
+ openssl
+ poppler
+ `(,util-linux "lib")
+ zlib))
+ (native-inputs (list doxygen git graphviz pkg-config))
+ (home-page "https://gdcm.sourceforge.net")
+ (synopsis "C++ library to read, parse, and write DICOM medical files")
+ (description
+ "@acronym{GDCM, Grassroots DICOM} implements the @acronym{DICOM, Digi=
tal
+Imaging and Communications in Medicine} standard to let researchers access
+clinical data directly. GDCM includes a file format definition and a netw=
ork
+communications protocol, both of which should be extended to provide a ful=
l set
+of tools for a researcher or small medical imaging vendor to interface wit=
h an
+existing medical database.")
+ (license license:bsd-3)))
+
(define-public mia
(package
(name "mia")
base-commit: e0ed305f2f096e7048af1a117c72895433f4886a
=2D-=20
2.38.1
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guix-patches@HIDDEN:bug#60640; Package guix-patches.
Full text available.Received: (at 60640) by debbugs.gnu.org; 10 Jan 2023 15:10:33 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jan 10 10:10:33 2023 Received: from localhost ([127.0.0.1]:40894 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pFGGn-0000At-12 for submit <at> debbugs.gnu.org; Tue, 10 Jan 2023 10:10:33 -0500 Received: from mail-ej1-f52.google.com ([209.85.218.52]:38606) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <tclaesson@HIDDEN>) id 1pFGGl-0000Ah-LX for 60640 <at> debbugs.gnu.org; Tue, 10 Jan 2023 10:10:32 -0500 Received: by mail-ej1-f52.google.com with SMTP id cf18so23094178ejb.5 for <60640 <at> debbugs.gnu.org>; Tue, 10 Jan 2023 07:10:31 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=cc:to:subject:message-id:date:from:in-reply-to:references :mime-version:from:to:cc:subject:date:message-id:reply-to; bh=0XAcTwNAjs4laFoKvc5Fb9Z/bZOpbMEKQfuLjjQGHiQ=; b=GzLmQ7YWjjIK2Uw/ABtduYvXlTlTLUZQW94L/FTmFxO+L1tzA7ynOwULmOso8G8yj4 nQ7LnAaZ8NUBtNFtJNiS12H00zzvFcIhsh72FDlcikKDUIye1M/kAmgeO85vPiEKRGgF fp9gvghKSJniwc1MIcxR1xkGo9/RePrkWY18NTZKea3UrjQzFL7iHdfKFPL55RNqQoeJ E4bJu8EAYALn9MmCE3QqgT2ipgz3+BeVNKfGbyEJq29A0uM72pTZ6Ow357KRPCTEJisi KovUpLDvVRm8K8+x/vc/X804yLyiHmAZdo4MMOgLAc/n+hdvWd131GmtJ63gpAWtUfLW W8tw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=cc:to:subject:message-id:date:from:in-reply-to:references :mime-version:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=0XAcTwNAjs4laFoKvc5Fb9Z/bZOpbMEKQfuLjjQGHiQ=; b=ZLFVZKfTCTLbmU/ibxxb8KUvH4t4hwnPCpYiWLkSAqmrhY0y/beZfaw0dlyK1/eSao gOEXOd6GpXXuAe8TpiyBgPP4PknlhhyJXxD2QbeXvPcfwKzmayncOekQQXokepcl1QTj Q6uUiBiwK4PcZX/i9F9XCs+x6rB0TUQJog8umAsqBwhgqbZLHwBUXa+BCzNCxXmeQ7eu iXifYis6kjunccTWvup7RFE6yPAOeCFwMpna5TEEua05ocoZeTDOp2TElQjCt3cAybPY SxsdPU/zNzPG573XNuWQCmn/3aBEnHK+CBoiEcvvIKjJHnRPJ7U85Dz7k/QNyXwclI7X WJuw== X-Gm-Message-State: AFqh2kqiborXbGkbn5W1QTfjNokSFHGYAaDLSD5n7x6mH5uR0gpal1Ff xz2zAjpQQH9mkc//MHYhqjKx8m2jCcIuA5q4sSg= X-Google-Smtp-Source: AMrXdXvrW3f/fiZutF58NZUgB+oZQFw5jhM2P5tamEVvfLdENXTbi4yGkPFxTjc2iDomDebeg1hNq5RKNg8g05L9dGI= X-Received: by 2002:a17:907:9d0d:b0:84d:4d2d:1c5f with SMTP id kt13-20020a1709079d0d00b0084d4d2d1c5fmr478661ejc.114.1673363425688; Tue, 10 Jan 2023 07:10:25 -0800 (PST) MIME-Version: 1.0 References: <877cxyp1wf.fsf@HIDDEN> <handler.60640.B.167314095112989.ack <at> debbugs.gnu.org> <87y1qdo3qq.fsf@HIDDEN> <87a62q1mca.fsf@nckx> In-Reply-To: <87a62q1mca.fsf@nckx> From: =?UTF-8?Q?Tor=2Dbj=C3=B6rn_Claesson?= <tclaesson@HIDDEN> Date: Tue, 10 Jan 2023 17:10:14 +0200 Message-ID: <CAO0k700WgGvQ7mtiS3RVUUfEAWXANjCmv+gaxK6j9yB12NL2Sg@HIDDEN> Subject: Re: [bug#60640] Acknowledgement (Gnu: Add gdcm) To: Tobias Geerinckx-Rice <me@HIDDEN> Content-Type: multipart/alternative; boundary="00000000000091800005f1ea48da" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60640 Cc: 60640 <at> debbugs.gnu.org, guix-patches@HIDDEN X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --00000000000091800005f1ea48da Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi! I'll answer your questions later, but have started the build > before I go out. > > The build appears to be running something like > > until fc-something; do :; done > > in an infinite loop, spamming the build log at best and slowing > down the build at worst. > > Did you notice that too? > I get a lot of "Fontconfig error: No writable cache directories" which appeared after adding graphviz as a native input for building documentation. Is this what you are meaning? Thanks=3D) Tor-bj=C3=B6rn --00000000000091800005f1ea48da Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div dir=3D"ltr"><div>Hi!</div><div><br></div><div><br></d= iv></div><div class=3D"gmail_quote"><blockquote class=3D"gmail_quote" style= =3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding= -left:1ex"> I'll answer your questions later, but have started the build <br> before I go out.<br> <br> The build appears to be running something like<br> <br> =C2=A0 until fc-something; do :; done<br> <br> in an infinite loop, spamming the build log at best and slowing <br> down the build at worst.<br> <br> Did you notice that too?<br></blockquote><div><br></div><div>I get a lot of= "Fontconfig error: No writable cache directories" which appeared= after adding graphviz as a native input for building documentation. Is thi= s what you are meaning?</div><div><br></div><div>Thanks=3D)</div><div>Tor-b= j=C3=B6rn<br></div></div></div> --00000000000091800005f1ea48da--
guix-patches@HIDDEN:bug#60640; Package guix-patches.
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I'll answer your questions later, but have started the build > before I go out. > > The build appears to be running something like > > until fc-something; do :; done > > in an infinite loop, spamming the build log at best and slowing > down the build at worst. > > Did you notice that too? > I get a lot of "Fontconfig error: No writable cache directories" which appeared after adding graphviz as a native input for building documentation. Is this what you are meaning? Thanks=3D) Tor-bj=C3=B6rn --00000000000091800005f1ea48da Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div dir=3D"ltr"><div>Hi!</div><div><br></div><div><br></d= iv></div><div class=3D"gmail_quote"><blockquote class=3D"gmail_quote" style= =3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding= -left:1ex"> I'll answer your questions later, but have started the build <br> before I go out.<br> <br> The build appears to be running something like<br> <br> =C2=A0 until fc-something; do :; done<br> <br> in an infinite loop, spamming the build log at best and slowing <br> down the build at worst.<br> <br> Did you notice that too?<br></blockquote><div><br></div><div>I get a lot of= "Fontconfig error: No writable cache directories" which appeared= after adding graphviz as a native input for building documentation. Is thi= s what you are meaning?</div><div><br></div><div>Thanks=3D)</div><div>Tor-b= j=C3=B6rn<br></div></div></div> --00000000000091800005f1ea48da--
guix-patches@HIDDEN:bug#60640; Package guix-patches.
Full text available.Received: (at 60640) by debbugs.gnu.org; 10 Jan 2023 14:42:19 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jan 10 09:42:19 2023 Received: from localhost ([127.0.0.1]:39205 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pFFpS-0007RM-LV for submit <at> debbugs.gnu.org; Tue, 10 Jan 2023 09:42:18 -0500 Received: from tobias.gr ([80.241.217.52]:42816) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <me@HIDDEN>) id 1pFFpR-0007RE-Fx for 60640 <at> debbugs.gnu.org; Tue, 10 Jan 2023 09:42:18 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; s=2018; bh=/GmR/vfYpXtr4 NjqzIKCTgzubPi/P4Wy/0cxmeXUrpA=; h=in-reply-to:date:subject:cc:to: from:references; d=tobias.gr; b=Stu7BMLIzUoEuXabGK+d0mDS76RF1a9IAvcnK/ FyMdr2a/ScdBq0PGto7waH+hqa4owFJslamE//IWwoKT5PpEGjvwgcAinZL/5z6uwqjxVk hE/3rLaT+PQAHV+E9WlU/UbHbLHcBFRN8MVi09qzXMngmscv+ZYKnKOvyed9iYzH+fxf+E RnxtYhQiHbIGoC5SmgEaF6bVgYmyhvlb+gnoqyWUIMgh2TIkfwt0Pq0QRssKKq8jg0f0Yi RLkhrW/pC/D5zTSeIDONuG0ipzH/Dyebsh5QeYu6ECnFstc8D0MW9YkLfSylQqBbDZvHfJ v/iwzz7XInPHXB0rRqXW23sQ== Received: by submission.tobias.gr (OpenSMTPD) with ESMTPSA id 1c724d1c (TLSv1.3:AEAD-AES256-GCM-SHA384:256:NO); Tue, 10 Jan 2023 14:42:10 +0000 (UTC) References: <877cxyp1wf.fsf@HIDDEN> <handler.60640.B.167314095112989.ack <at> debbugs.gnu.org> <87y1qdo3qq.fsf@HIDDEN> From: Tobias Geerinckx-Rice <me@HIDDEN> To: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN> Subject: Re: [bug#60640] Acknowledgement (Gnu: Add gdcm) Date: Tue, 10 Jan 2023 15:40:50 +0100 In-reply-to: <87y1qdo3qq.fsf@HIDDEN> BIMI-Selector: v=BIMI1; s=default; Message-ID: <87a62q1mca.fsf@nckx> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 60640 Cc: 60640 <at> debbugs.gnu.org, guix-patches@HIDDEN X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable Hi again, Tor-bj=C3=B6rn Claesson =E5=86=99=E9=81=93=EF=BC=9A > This patch adds GDCM (a nice C++ library for DICOM, as in=20 > medical imaging), > with a few wharts: I'll answer your questions later, but have started the build=20 before I go out. The build appears to be running something like until fc-something; do :; done in an infinite loop, spamming the build log at best and slowing=20 down the build at worst. Did you notice that too? Kind regards, T G-R --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iIMEARYKACsWIQT12iAyS4c9C3o4dnINsP+IT1VteQUCY715pQ0cbWVAdG9iaWFz LmdyAAoJEA2w/4hPVW15gaQBAI8MpZ0upjkClTQxcOnUeGB6B6RADv70GT7BAjbl stdTAP9vG1MdAKL1lRJ9GhnrXLintk6Qt/TR9+1uJDER42a8BQ== =ZPxT -----END PGP SIGNATURE----- --=-=-=--
guix-patches@HIDDEN:bug#60640; Package guix-patches.
Full text available.Received: (at submit) by debbugs.gnu.org; 10 Jan 2023 14:42:34 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jan 10 09:42:34 2023 Received: from localhost ([127.0.0.1]:39209 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pFFpi-0007Rr-0g for submit <at> debbugs.gnu.org; Tue, 10 Jan 2023 09:42:34 -0500 Received: from lists.gnu.org ([209.51.188.17]:50756) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <me@HIDDEN>) id 1pFFpg-0007Rc-Gd for submit <at> debbugs.gnu.org; Tue, 10 Jan 2023 09:42:32 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <me@HIDDEN>) id 1pFFpV-0003gu-Tp for guix-patches@HIDDEN; Tue, 10 Jan 2023 09:42:21 -0500 Received: from tobias.gr ([80.241.217.52]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <me@HIDDEN>) id 1pFFpU-00032x-En for guix-patches@HIDDEN; Tue, 10 Jan 2023 09:42:21 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; s=2018; bh=/GmR/vfYpXtr4 NjqzIKCTgzubPi/P4Wy/0cxmeXUrpA=; h=in-reply-to:date:subject:cc:to: from:references; d=tobias.gr; b=Stu7BMLIzUoEuXabGK+d0mDS76RF1a9IAvcnK/ FyMdr2a/ScdBq0PGto7waH+hqa4owFJslamE//IWwoKT5PpEGjvwgcAinZL/5z6uwqjxVk hE/3rLaT+PQAHV+E9WlU/UbHbLHcBFRN8MVi09qzXMngmscv+ZYKnKOvyed9iYzH+fxf+E RnxtYhQiHbIGoC5SmgEaF6bVgYmyhvlb+gnoqyWUIMgh2TIkfwt0Pq0QRssKKq8jg0f0Yi RLkhrW/pC/D5zTSeIDONuG0ipzH/Dyebsh5QeYu6ECnFstc8D0MW9YkLfSylQqBbDZvHfJ v/iwzz7XInPHXB0rRqXW23sQ== Received: by submission.tobias.gr (OpenSMTPD) with ESMTPSA id 1c724d1c (TLSv1.3:AEAD-AES256-GCM-SHA384:256:NO); Tue, 10 Jan 2023 14:42:10 +0000 (UTC) References: <877cxyp1wf.fsf@HIDDEN> <handler.60640.B.167314095112989.ack <at> debbugs.gnu.org> <87y1qdo3qq.fsf@HIDDEN> From: Tobias Geerinckx-Rice <me@HIDDEN> To: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN> Subject: Re: [bug#60640] Acknowledgement (Gnu: Add gdcm) Date: Tue, 10 Jan 2023 15:40:50 +0100 In-reply-to: <87y1qdo3qq.fsf@HIDDEN> BIMI-Selector: v=BIMI1; s=default; Message-ID: <87a62q1mca.fsf@nckx> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Received-SPF: pass client-ip=80.241.217.52; envelope-from=me@HIDDEN; helo=tobias.gr X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.6 (-) X-Debbugs-Envelope-To: submit Cc: 60640 <at> debbugs.gnu.org, guix-patches@HIDDEN X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -2.6 (--) --=-=-= Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable Hi again, Tor-bj=C3=B6rn Claesson =E5=86=99=E9=81=93=EF=BC=9A > This patch adds GDCM (a nice C++ library for DICOM, as in=20 > medical imaging), > with a few wharts: I'll answer your questions later, but have started the build=20 before I go out. The build appears to be running something like until fc-something; do :; done in an infinite loop, spamming the build log at best and slowing=20 down the build at worst. Did you notice that too? Kind regards, T G-R --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iIMEARYKACsWIQT12iAyS4c9C3o4dnINsP+IT1VteQUCY715pQ0cbWVAdG9iaWFz LmdyAAoJEA2w/4hPVW15gaQBAI8MpZ0upjkClTQxcOnUeGB6B6RADv70GT7BAjbl stdTAP9vG1MdAKL1lRJ9GhnrXLintk6Qt/TR9+1uJDER42a8BQ== =ZPxT -----END PGP SIGNATURE----- --=-=-=--
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Date: Tue, 10 Jan 2023 07:01:42 +0000
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Subject: Re: [bug#60640] Acknowledgement (Gnu: Add gdcm)
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--ed3932af558e7c8e83140b5f95bc497c3c8dfdf394716b5c117c3ea1159c
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On Mon Jan 9, 2023 at 10:50 AM GMT, Tor-bj=C3=B6rn Claesson wrote:
> No failures, only guix lint tells me "gdcm@HIDDEN: label 'util-linux'
> does not match package name 'util-linux:lib'", so I thought I might be
> doing something wrong. If not then all fine on that front.
Oh, that's fine. I don't think there's a way to fix that at the moment.
-- (
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guix-patches@HIDDEN:bug#60640; Package guix-patches.
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[212.90.81.204]) by smtp.gmail.com with ESMTPSA id c21-20020ac244b5000000b004cb015794a8sm1558576lfm.109.2023.01.09.02.53.39 for <60640 <at> debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 09 Jan 2023 02:53:39 -0800 (PST) References: <877cxyp1wf.fsf@HIDDEN> <handler.60640.B.167314095112989.ack <at> debbugs.gnu.org> <87y1qdo3qq.fsf@HIDDEN> <CAO0k700SJqxsqHXjr=XOWijdeBvjeQzxW40E5pb+18d8sUXPig@HIDDEN> <604C2BA9-1D59-4560-BE33-285FB879C3AA@HIDDEN> User-agent: mu4e 1.8.13; emacs 28.2 From: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN> To: 60640 <at> debbugs.gnu.org Subject: Re: [bug#60640] Acknowledgement (Gnu: Add gdcm) Date: Mon, 09 Jan 2023 12:50:32 +0200 In-reply-to: <604C2BA9-1D59-4560-BE33-285FB879C3AA@HIDDEN> Message-ID: <87cz7oc72l.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60640 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hi Tobias, thanks for taking the time to comment! Tobias Geerinckx-Rice <me@HIDDEN> writes: > Hi Tor-bj=C3=B6rn, > > On 8 January 2023 08:04:40 UTC, "Tor-bj=C3=B6rn Claesson" <tclaesson@gmai= l.com> wrote: >>Den s=C3=B6n 8 jan. 2023 kl 10:00 skrev Tor-bj=C3=B6rn Claesson <tclaesso= n@HIDDEN>: >> >>> >>> 5. I'm not sure how to specify util-linux:bin as an input? >>> >>I mean util-linux:lib... > > Exactly like you did. Are you seeing util-linux-related failures? > > > Kind regards, > > T G-R > > Sent on the go. Excuse or enjoy my brevity. No failures, only guix lint tells me "gdcm@HIDDEN: label 'util-linux' does not match package name 'util-linux:lib'", so I thought I might be doing something wrong. If not then all fine on that front. --=20 Cheers, Tor-bj=C3=B6rn Claesson
guix-patches@HIDDEN:bug#60640; Package guix-patches.
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Mon, 9 Jan 2023 08:28:23 +0000 (UTC) Date: Mon, 09 Jan 2023 08:28:29 +0000 From: Tobias Geerinckx-Rice <me@HIDDEN> To: guix-patches@HIDDEN, =?ISO-8859-1?Q?Tor-bj=F6rn_Claesson?= <tclaesson@HIDDEN>, 60640 <at> debbugs.gnu.org Subject: Re: [bug#60640] Acknowledgement (Gnu: Add gdcm) In-Reply-To: <CAO0k700SJqxsqHXjr=XOWijdeBvjeQzxW40E5pb+18d8sUXPig@HIDDEN> References: <877cxyp1wf.fsf@HIDDEN> <handler.60640.B.167314095112989.ack <at> debbugs.gnu.org> <87y1qdo3qq.fsf@HIDDEN> <CAO0k700SJqxsqHXjr=XOWijdeBvjeQzxW40E5pb+18d8sUXPig@HIDDEN> Message-ID: <604C2BA9-1D59-4560-BE33-285FB879C3AA@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Autocrypt: addr=me@HIDDEN; prefer-encrypt=mutual; keydata= mQINBFVks2ABEACjGBPhWf/qx0L9OhEIrAFTimo5dHa1FLy0AHaHvxmwYSIdJmERYGiNle1rcOvw cFRtu8KJUsrs27Vgoso3qHJpghVitUUf0v3ZuXQT9kfuQLz1Y8pyMzHwVFMLiJVj4Z3y7CJk+xyZ cpSAMbyPINbFVEhsK+z+8ojVGuaiucZkib6b67ySG6Pp1bon8xVvosj71ZRjfXh1t4X8laWO7fQq itT9lmc6DxbE/4vIhR+Vb2MblaA+DyHoNHGGao89h4CO99lfzWzsux41DnEG9d317sJRQTig6Wja EKHXZRA9FbfogD4SDa2uQYCpTJpsVjAyZyu2fuJ+t0zJJ+Ai9qDY87P6hOyd+/n8Eh2Y4TbxJiDo XUT72XY/RfPH1qrMIP3EI/NNL4LQeGG1n+625k3OVWcRVXG2vRrB6qurLmGkLEmjXWCFD9cCRGfH LeajLm9sM+t/nZPZ3btetcmK9tM2EwivyLUNhrTk73UUnI4CSAzdO2cISqo9zSMtFgj2alqd2fOR s7CKfEn+5PquruDbp/Ej7dOOrjgWSCXLDDYXRrtaKrLz/dhqq5ftFYi9tUTTQecFotM08fPtu+Kw JMP2ySHCkUqp0GvrUCeSRPAJZsmJrd535y+LlRhnqb0mbG4dgMa8A6xhkFYugnqldy/q7kX1EmRI 686N7bA6fh1MCQARAQABtCRUb2JpYXMgR2VlcmluY2t4LVJpY2UgPG1lQHRvYmlhcy5ncj6JAlIE EwEKADwCHgECF4ACGQECGwMWIQT1vFU0w28Ah7OdNu8cncT+udt8SwUCXpe0rAYLCQgHCgQFFQoJ CAsFFgMCAQAACgkQHJ3E/rnbfEu5IhAAk+0BW/twLmx1xMmeXn+I7Ne6SG3++0TRBduEaGWV3n59 lX6XPZUQdAPpS4uy0H+c90Owkw+aWUEwfyOWphrxZRtR2cCOP/3Pxj3Vgtz5RkY4u27lMj15jqa/ p7l2l256ZKJOegr9TvOWtkhMp5lxeVHT6f/44Kv/r/8mMCgSnLXYrEWPE462xI+mIJOanHLJb6No f2xLRCvXoLLp7Yejjv1dwOO71R9PMRhtNy46pZM1ylQ++UTkeSocJw4aNtiu0DHOkX9AlNBkutIx x07RpO+MqJKlzzLeQiC/fE5+dR2itRONopwXAqN3MuT7MonQo5XifBn+VK8i9xZWTXZDkWItWtCC 8oIj4zwxwFWiTmMwwSbI3Wdd/11Zw3CLc4Gd0M6NVgvAnuErQXSgr4lrWhZcncvi4L6EJTc9AUSa 8UWPF+S9t+CHTukpJmcYnsccMkOBhT7OZlmWBsylrYK/JTRWqgWSHWdSKmOuLK+MGDneOZEHkEcf jeXRWvmG7MSU5tE/p7NDLIg9vkvhQV9b0q4OtY65uNWbRe2QRJaYMDcYUAeSZzivRa8VaoVen6tb FvH44zpCxubn23ABl9YIzwvJC++r+H2qLdLpy0cfITiZadZ74Ae0aosNw7XARS6OY+A03BfXyPiI 2oW0jf/PdH9sh2mQrQxIQJ5cZz6Z3X20MFRvYmlhcyBHZWVyaW5ja3gtUmljZSAodG9iaWFzLmdy KSA8bWVAdG9iaWFzLmdyPokCNgQwAQoAIBYhBPW8VTTDbwCHs5027xydxP6523xLBQJZUuJkAh0g AAoJEBydxP6523xLwEoP/iaVWdICefmaZ+bkdUg6hwTKxSPlYdLoaCxYI5V2NnZYXG0dy47E7WJP 4EmTDldcne4UG5NyCgXPSMZDNMqcddEMNbmlssTcLKyu6R/VvTcuL3pEhNoLzm9t2IHR/YGAHJIc pyfmJ3amGSlsbo6s6Vv+mbrJTRPIDpLUst/PDoGYihcSKTxoIw8RtNAy+FAliIdJ8ZuPA3BTxQei sQzgWJo68UInvnFp4juq0zupNDqKddemI8kZCRK/fFPBDD71nqiSJjx2tvbjkTiPU9gmTp7Nulgj ZATZIt0pUhn87w15ItzrsiEjTYCMTmHY5wnvyLarFKZLzQjgUJfsbv4WRJRnX0/EEJWMvMtSdtXL fjwTLrSGAr4vh13PMfE6uVkGkeCV/8BfGJqRE4zkI+QOVILw6VSAP6sdtGSGb52bcCuPj7p9zGIB IuKFudT+DzUb5uV2jbahSjJ8X4Ak/ruG2Hv3iICZawDpHV1JDNgY910KNi5T6gFrjFA2G6aiXDCO SlToLPnPBYH85UVOsp2VykE9AREKS7a7o76cibjwBNN+4xJqJRxhs9YH4JKzE3w/ptVnx49QFBGc pjPkzMTs7DtanD8iqL4J6afnycv9KqIlNJONaMHvzxeunV7QCsoF6DdusZJKFMexiDBaOFUmGFFS XfzK2oNjknx1QApyTPvh X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 60640 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hi Tor-bj=C3=B6rn, On 8 January 2023 08:04:40 UTC, "Tor-bj=C3=B6rn Claesson" <tclaesson@gmail= =2Ecom> wrote: >Den s=C3=B6n 8 jan=2E 2023 kl 10:00 skrev Tor-bj=C3=B6rn Claesson <tclaes= son@gmail=2Ecom>: > >> >> 5=2E I'm not sure how to specify util-linux:bin as an input? >> >I mean util-linux:lib=2E=2E=2E Exactly like you did=2E Are you seeing util-linux-related failures? Kind regards, T G-R Sent on the go=2E Excuse or enjoy my brevity=2E
guix-patches@HIDDEN:bug#60640; Package guix-patches.
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Kind regards, T G-R Sent on the go=2E Excuse or enjoy my brevity=2E
guix-patches@HIDDEN:bug#60640; Package guix-patches.
Full text available.Received: (at 60640) by debbugs.gnu.org; 8 Jan 2023 08:05:00 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Jan 08 03:05:00 2023 Received: from localhost ([127.0.0.1]:59784 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pEQfs-000845-DD for submit <at> debbugs.gnu.org; Sun, 08 Jan 2023 03:05:00 -0500 Received: from mail-ed1-f48.google.com ([209.85.208.48]:34436) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <tclaesson@HIDDEN>) id 1pEQfq-00083r-DK for 60640 <at> debbugs.gnu.org; Sun, 08 Jan 2023 03:04:58 -0500 Received: by mail-ed1-f48.google.com with SMTP id z11so8146365ede.1 for <60640 <at> debbugs.gnu.org>; Sun, 08 Jan 2023 00:04:58 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=to:subject:message-id:date:from:in-reply-to:references:mime-version :from:to:cc:subject:date:message-id:reply-to; bh=9htsSlwYTd+xqIFDMVWMmSvIRSdxlqs84rDd72pbkvg=; b=hl2Xq0I5QFAtJe61708awNgbhB1MWUjEKupKNH2YuZBEP9ISQW5bgBPLav5+WgHQTW exWxreObwAIxnUhjJTIs1NYd9VmX3VmbBpFkZrXnemQcjwYgCUq6yuj3Uy+19Y0t6Vkj RIqcpNHq8jYumbhOBvHXb8Ut5tM8REQ1EMu3rGrXar95K3MuR5nwjYJPxCpRZ65CY/1q eCUgQJsYP1NGLOCl1ba2oMu/kIfbx0VPrLNqGF7Zh0qF9Phdab7SqmaIvBgGd3vChHKC o4T9MvSyS7BjcIvHMSbx14wnykBp7iwcbzLoyB1hOIiL4feeE9Orhcvrtd22F6tJTIJv 2haw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=to:subject:message-id:date:from:in-reply-to:references:mime-version :x-gm-message-state:from:to:cc:subject:date:message-id:reply-to; bh=9htsSlwYTd+xqIFDMVWMmSvIRSdxlqs84rDd72pbkvg=; b=NqrbH+F/w42krUDgNePghe0sQwy0IOsmG2M277MbvGFFflu9CNkD383Tb7QxMn9MOY U/wdW1QAfyqlYK8eXJR2KDjA1sqeNGjPRP+2y6O9QlnlOylqyefwc3ZdAonQa/bIB4E1 VVcreAMWt/Ed5RHts+iCwK3IXLdZAaXx6M3IpRNqgjDYmqyx4jIQ1duhzbYiML4JAuU/ V9N+8+bgONyUGwd61yH+A0OxxsDcOmzNPZBFpYpZ4x0Rg1plmMT8wPhHWg63KXCxtg8F 9RrY+Hn5iDjHfJ8O8C4rfbg4Q7HaoCHMftr9pnJbaCBVS/fCGIlyS812W18mo/IUYQKi XBmw== X-Gm-Message-State: AFqh2koZ+OAfa0xmoFPi2WM/il1jCPNEWlxLvI3d7jcj+K8uF6X8kBj3 5bH4l4w/+EsB4SduKWcBoVABgS157Fb/F1dSh8XugddQ X-Google-Smtp-Source: AMrXdXu1u05oDkPkmeB74jpEFe3PfQtcGj5W3eCnRu3U/N1fHYuNZFbL+F0tdY//RSU+FIOqb3tbnmxFgHm98FfjZJc= X-Received: by 2002:a50:8710:0:b0:47d:de33:4a6e with SMTP id i16-20020a508710000000b0047dde334a6emr5941381edb.101.1673165092164; Sun, 08 Jan 2023 00:04:52 -0800 (PST) MIME-Version: 1.0 References: <877cxyp1wf.fsf@HIDDEN> <handler.60640.B.167314095112989.ack <at> debbugs.gnu.org> <87y1qdo3qq.fsf@HIDDEN> In-Reply-To: <87y1qdo3qq.fsf@HIDDEN> From: =?UTF-8?Q?Tor=2Dbj=C3=B6rn_Claesson?= <tclaesson@HIDDEN> Date: Sun, 8 Jan 2023 10:04:40 +0200 Message-ID: <CAO0k700SJqxsqHXjr=XOWijdeBvjeQzxW40E5pb+18d8sUXPig@HIDDEN> Subject: Re: bug#60640: Acknowledgement (Gnu: Add gdcm) To: 60640 <at> debbugs.gnu.org Content-Type: multipart/alternative; boundary="000000000000f8186d05f1bc1ad1" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60640 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --000000000000f8186d05f1bc1ad1 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Den s=C3=B6n 8 jan. 2023 kl 10:00 skrev Tor-bj=C3=B6rn Claesson <tclaesson@= gmail.com>: > > 5. I'm not sure how to specify util-linux:bin as an input? > I mean util-linux:lib... --000000000000f8186d05f1bc1ad1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div dir=3D"ltr"><br></div><br><div class=3D"gmail_quote">= <div dir=3D"ltr" class=3D"gmail_attr">Den s=C3=B6n 8 jan. 2023 kl 10:00 skr= ev Tor-bj=C3=B6rn Claesson <<a href=3D"mailto:tclaesson@HIDDEN">tclae= sson@HIDDEN</a>>:<br></div><blockquote class=3D"gmail_quote" style=3D= "margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-le= ft:1ex"><br> 5. I'm not sure how to specify util-linux:bin as an input?<br></blockqu= ote><div>I mean util-linux:lib... <br></div></div></div> --000000000000f8186d05f1bc1ad1--
guix-patches@HIDDEN:bug#60640; Package guix-patches.
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[212.90.81.204]) by smtp.gmail.com with ESMTPSA id dt17-20020a0565122a9100b004cb061887b5sm943798lfb.126.2023.01.08.00.00.14 for <60640 <at> debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 08 Jan 2023 00:00:14 -0800 (PST) References: <877cxyp1wf.fsf@HIDDEN> <handler.60640.B.167314095112989.ack <at> debbugs.gnu.org> User-agent: mu4e 1.8.13; emacs 28.2 From: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN> To: 60640 <at> debbugs.gnu.org Subject: Re: bug#60640: Acknowledgement (Gnu: Add gdcm) Date: Sun, 08 Jan 2023 09:59:40 +0200 In-reply-to: <handler.60640.B.167314095112989.ack <at> debbugs.gnu.org> Message-ID: <87y1qdo3qq.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60640 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hi! This patch adds GDCM (a nice C++ library for DICOM, as in medical imaging), with a few wharts: 1. I have not yet been able to build the bin output, which consists of utilities for manipulating DICOM data.=20 2. It does not build pdf-documentation, since that would require texlive as a native input. 3. It does not perform tests. 4. It uses socketxx, ljpeg and papyrus3 from the gdcm sources.=20 5. I'm not sure how to specify util-linux:bin as an input? Cheers, Tor-bj=C3=B6rn Claesson help-debbugs@HIDDEN (GNU bug Tracking System) writes: > Thank you for filing a new bug report with debbugs.gnu.org. > > This is an automatically generated reply to let you know your message > has been received. > > Your message is being forwarded to the package maintainers and other > interested parties for their attention; they will reply in due course. > > Your message has been sent to the package maintainer(s): > guix-patches@HIDDEN > > If you wish to submit further information on this problem, please > send it to 60640 <at> debbugs.gnu.org. > > Please do not send mail to help-debbugs@HIDDEN unless you wish > to report a problem with the Bug-tracking system. --=20 Mvh, Tor-bj=C3=B6rn Claesson
guix-patches@HIDDEN:bug#60640; Package guix-patches.
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From: =?utf-8?Q?Tor-bj=C3=B6rn?= Claesson <tclaesson@HIDDEN>
To: guix-patches@HIDDEN
Subject: Gnu: Add gdcm
Date: Sat, 07 Jan 2023 21:40:42 +0200
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gnu/packages/image-processing.scm | 72 +++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 70c820e76b..271593b5f9 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -99,6 +99,7 @@ (define-module (gnu packages image-processing)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
#:use-module (gnu packages video)
+ #:use-module (gnu packages web)
#:use-module (gnu packages xiph)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@@ -1776,3 +1777,74 @@ (define-public charls
to have them encoded to JPEG-LS, or JPEG-LS streams, which CharLS will decode
to images.")
(license license:bsd-3)))
+
+(define-public gdcm
+ (package
+ (name "gdcm")
+ (version "3.0.20")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/malaterre/GDCM/")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))))
+ (build-system cmake-build-system)
+ (outputs '("out" "doc"))
+ (arguments
+ (list #:tests? #f
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'configure 'set-LDFLAGS
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "LDFLAGS"
+ (string-append "-Wl,-rpath="
+ #$output "/lib"))))
+ (add-before 'build 'patch-gdcm-charls.h
+ (lambda _
+ (substitute* "../source/Utilities/gdcm_charls.h"
+ (("# include <CharLS/charls.h>")
+ "# include <charls/charls.h>")) #t)))
+ #:configure-flags #~(list "-DCMAKE_SKIP_RPATH:BOOL=YES"
+ "-DCMAKE_BUILD_TYPE:STRING=Release"
+ "-DCMAKE_C_FLAGS=-fvisibility=hidden"
+ "-DCMAKE_CXX_FLAGS=-fvisibility=hidden"
+ "-DGDCM_BUILD_SHARED_LIBS:BOOL=ON"
+ "-DGDCM_DOCUMENTATION:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_EXPAT:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_ZLIB:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_CHARLS:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_POPPLER:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_JSON:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_UUID:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=ON"
+ "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=ON"
+ "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF"
+ "-DGCM_BUILD_TESTING:BOOL=OFF"
+ "-DGDCM_BUILD_APPLICATIONS:BOOL=OFF"
+ "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=OFF"
+ "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=OFF"
+ "-DGDCM_USE_SYSTEM_LJPEG:BOOL=OFF")))
+ (inputs (list openssl
+ expat
+ charls
+ poppler
+ libxml2
+ json-c
+ openjpeg
+ `(,util-linux "lib")
+ zlib))
+ (native-inputs (list git pkg-config doxygen graphviz))
+ (home-page "https://gdcm.sourceforge.net")
+ (synopsis
+ "C++ library dedicated to reading/parsing and writing DICOM medical files")
+ (description
+ "Grassroots DICOM (GDCM) is an implementation of the DICOM standard
+designed to be open source so that researchers may access clinical data
+directly. GDCM includes a file format definition and a network communications
+protocol, both of which should be extended to provide a full set of tools for
+a researcher or small medical imaging vendor to interface with an existing
+medical database.")
+ (license license:bsd-3)))
--
2.38.1
Tor-björn Claesson <tclaesson@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#60640; Package guix-patches.
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