guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 7b2b2ed2f2a5c93fb9352f2795764d52525db8ef
Author: Jake Forster <[email protected]>
AuthorDate: Sun Oct 12 01:04:19 2025 +1030
gnu: gdcm: Update to 3.2.2.
* gnu/packages/bioinformatics.scm (gdcm): Update to 3.2.2.
[arguments]<#:test-exclude>: Do not exclude TestFileMetaInformation and
TestElement2; exclude TestImageReaderRandomEmpty and TestTransferSyntax.
<#:configure-flags>: Add "-DGDCM_BUILD_DOCBOOK_MANPAGES=ON".
[home-page]: Update.
Change-Id: I895dea12d4237d29f9f7d826f0a0d65f10f7e116
Signed-off-by: Sharlatan Hellseher <[email protected]>
---
gnu/packages/bioinformatics.scm | 26 ++++++++++++++------------
1 file changed, 14 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1e5108335e..5a5ea40a6e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -25302,7 +25302,7 @@ module capable of computing base-level alignments for
very large sequences.")
(define-public gdcm
(package
(name "gdcm")
- (version "3.0.20")
+ (version "3.2.2")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -25312,14 +25312,12 @@ module capable of computing base-level alignments for
very large sequences.")
(file-name (git-file-name name version))
(sha256
(base32
- "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l"))))
+ "1d9dm1wawgjy6vgw3shqchqpjcic6hprwhn0v7dw1qkgn3y8508w"))))
(build-system cmake-build-system)
(outputs '("out" "doc"))
(arguments
(list
- #:test-exclude (string-join (list "TestFileMetaInformation"
- "TestElement2"
- "TestSCUValidation"
+ #:test-exclude (string-join (list "TestSCUValidation"
"TestWriter"
"TestAnonymizer4"
"TestPrinter1"
@@ -25329,23 +25327,27 @@ module capable of computing base-level alignments for
very large sequences.")
"TestStrictScanner2_1"
"TestStrictScanner2"
"TestStrictScanner2_2"
- "TestFind")
+ "TestFind"
+ ;; Fail with 'Unsupported JPEG data
precision 12'.
+ "TestImageReaderRandomEmpty"
+ "TestTransferSyntax")
"|")
#:configure-flags
- #~(list "-DGDCM_BUILD_TESTING=true"
+ #~(list "-DGDCM_BUILD_DOCBOOK_MANPAGES=ON"
+ "-DGDCM_BUILD_TESTING=true"
"-DGDCM_DOCUMENTATION:BOOL=ON"
- "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF"
(string-append "-DGDCM_INSTALL_DOC_DIR="
- #$output:doc "/share/doc/" #$name))
+ #$output:doc "/share/doc/" #$name)
+ "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF")
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'set-HOME
- ;; The build spams ‘Fontconfig error: No writable cache
- ;; directories’ in a seemingly endless loop otherwise.
+ ;; The build with documentation spams ‘Fontconfig error: No
writable
+ ;; cache directories’ in a seemingly endless loop otherwise.
(lambda _
(setenv "HOME" "/tmp"))))))
(native-inputs (list docbook-xsl doxygen graphviz libxslt))
- (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page";)
+ (home-page "https://sourceforge.net/projects/gdcm/";)
(synopsis "Grassroots DICOM library")
(description
"Grassroots DICOM (GDCM) is an implementation of the DICOM standard
