diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0825fbb6efd..473e91bda9f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7941,7 +7941,7 @@ similarity of community members.") (add-after 'unpack 'chdir (lambda _ (chdir "python")))))) - (inputs (list hdf5)) + (inputs (list hdf5-1.10)) (propagated-inputs (list python-dateutil)) (native-inputs @@ -11349,7 +11349,7 @@ simultaneously.") (install-file "libs/kfg/default.kfg" target) (install-file "libs/kfg/certs.kfg" target))))))) (inputs - (list file hdf5 java-ngs libxml2 ngs-sdk )) + (list file hdf5-1.10 java-ngs libxml2 ngs-sdk )) (native-inputs (list perl)) ;; NCBI-VDB requires SSE capability. (supported-systems '("i686-linux" "x86_64-linux")) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8522eb07a55..4e96d70849e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14934,7 +14934,7 @@ dendrograms.") "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs - (list zlib hdf5)) + (list zlib hdf5-1.10)) (native-inputs (list r-knitr r-testthat which)) (propagated-inputs diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 89e7ef83e60..83b694b4096 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1389,7 +1389,7 @@ graphics image formats like PNG, BMP, JPEG, TIFF and others.") `(("boost" ,boost) ("fftw" ,fftw) ("fftwf" ,fftwf) - ("hdf5" ,hdf5) + ("hdf5" ,hdf5-1.10) ("ilmbase" ,ilmbase) ; propagated by openexr, but needed explicitly ; to create a configure-flag ("libjpeg" ,libjpeg-turbo) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3de5b7b8ae2..4f2cfa414ab 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1834,7 +1834,7 @@ extremely large and complex data collections.") (base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00")) (patches (search-patches "hdf5-config-date.patch")))))) -(define-public hdf5-1.14 +(define-public hdf5 (package (inherit hdf5-1.8) (version "1.14.3") @@ -1872,10 +1872,6 @@ extremely large and complex data collections.") (("@UNAME_INFO@") "Linux")))))))))) -(define-public hdf5 - ;; Default version of HDF5. - hdf5-1.10) - ;; Keep this in sync with the current hdf5 package. (define-public hdf-java (package @@ -2041,7 +2037,7 @@ System (Grid, Point and Swath).") (list autoconf automake gfortran libtool)) (build-system gnu-build-system) (inputs - (list hdf5-1.14 zlib gctp)) + (list hdf5 zlib gctp)) (arguments (list #:configure-flags ''("--enable-install-include" "--enable-shared" @@ -2076,13 +2072,13 @@ Swath).") (license (license:non-copyleft home-page)))) (define-public hdf5-parallel-openmpi - (package/inherit hdf5-1.14 ;use the latest + (package/inherit hdf5 (name "hdf5-parallel-openmpi") (inputs `(("mpi" ,openmpi) ,@(package-inputs hdf5))) (arguments - (substitute-keyword-arguments (package-arguments hdf5-1.14) + (substitute-keyword-arguments (package-arguments hdf5) ((#:configure-flags flags) #~(cons "--enable-parallel" (delete "--enable-cxx" @@ -10630,7 +10626,7 @@ computation is supported via MPI.") curl fftw gettext-minimal - hdf5-1.14 + hdf5 libarchive libx11 libxml2