ninja: build stopped: subcommand failed. * ERROR: sci-libs/hdf5-1.12.1::gentoo failed (compile phase): * ninja -v -j3 -l0 failed * * Call stack: ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1_desktop-j3-20210813-003635 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-11.2.0 * clang version 12.0.1 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/12/bin /usr/lib/llvm/12 12.0.1 Python 3.9.6 Available Ruby profiles: [1] ruby26 (with Rubygems) [2] ruby30 (with Rubygems) * Available Rust versions: [1] rust-1.54.0 * The following VMs are available for generation-2: Available Java Virtual Machines: (none found) The Glorious Glasgow Haskell Compilation System, version 8.10.4 HEAD of ::gentoo commit 208f7cdcb3b3be74aeaa88a099e5904ba536773f Author: Repository mirror & CI <repomirrorci@gentoo.org> Date: Mon Aug 16 18:21:43 2021 +0000 2021-08-16 18:21:42 UTC emerge -qpvO sci-libs/hdf5 [ebuild U ] sci-libs/hdf5-1.12.1 [1.10.5-r1] USE="fortran hl zlib -cxx -debug -doc% -examples (-mpi) -szip -test% -threads -unsupported"
Created attachment 733366 [details] emerge-info.txt
Created attachment 733369 [details] emerge-history.txt
Created attachment 733372 [details] environment
Created attachment 733375 [details] etc.portage.tar.bz2
Created attachment 733378 [details] logs.tar.bz2
Created attachment 733381 [details] sci-libs:hdf5-1.12.1:20210816-193359.log.bz2
Created attachment 733384 [details] temp.tar.bz2
same here.
Actual error: Error: Symbol ‘h5i_invalid_hid_f’ at (1) has no IMPLICIT type. Please change the subject accordingly
same here
I have: FAILED: fortran/src/CMakeFiles/hdf5_fortran-static.dir/H5Lff.F90.o bin/static/h5l.mod /usr/bin/x86_64-pc-linux-gnu-gfortran -I/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortr an/src -I/usr/include -I/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src -I/var/tm p/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1_build/bin/static -I/var/tmp/portage/sci-libs/hdf5-1. 12.1/work/hdf5-1.12.1_build/fortran -I/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1_build/f ortran/src -I/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1_build/src -I/var/tmp/portage/sci -libs/hdf5-1.12.1/work/hdf5-1.12.1/src -O2 -march=native -pipe -O2 -march=native -pipe -fdiagnostics -urls=never -fno-diagnostics-color -Jbin/static -fPIC -Waliasing -Wall -Wcharacter-truncation -Wextr a -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -ffree-form -fimplicit-none -std=f2008 -Wa rray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wre alloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -fpreprocessed -o fortran/src/CMakeFiles/hdf5_fortra n-static.dir/H5Lff.F90.o -c fortran/src/CMakeFiles/hdf5_fortran-static.dir/H5Lff.F90-pp.f90 /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:49:28: 49 | TYPE(H5O_TOKEN_T_F) :: token | 1 Error: Derived type at (1) has not been previously defined and so cannot appear in a derived type definition /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:644:24: 644 | TYPE(H5O_TOKEN_T_F), INTENT(OUT), TARGET :: token ! If the link is a hard link, token specifies the object token that the link points to | 1 Error: Derived type ‘h5o_token_t_f’ at (1) is being used before it is defined /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:660:47: 660 | IMPORT :: HID_T, SIZE_T, H5O_TOKEN_T_F | 1 Error: Cannot IMPORT ‘h5o_token_t_f’ from host scoping unit at (1) - does not exist. /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:667:29: 667 | TYPE(H5O_TOKEN_T_F), INTENT(OUT) :: token | 1 Error: Derived type ‘h5o_token_t_f’ at (1) is being used before it is defined /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:753:24: 753 | TYPE(H5O_TOKEN_T_F), INTENT(OUT), TARGET :: token ! If the link is a hard link, token specifies the object token that the link points to | 1 Error: Derived type ‘h5o_token_t_f’ at (1) is being used before it is defined /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:771:56: 771 | IMPORT :: HID_T, SIZE_T, HSIZE_T, H5O_TOKEN_T_F | 1 Error: Cannot IMPORT ‘h5o_token_t_f’ from host scoping unit at (1) - does not exist. /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:783:29: 783 | TYPE(H5O_TOKEN_T_F), INTENT(OUT) :: token | 1 Error: Derived type ‘h5o_token_t_f’ at (1) is being used before it is defined /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:730:53: 730 | link_type, f_corder_valid, corder, cset, token, val_size, hdferr, lapl_id) | 1 Error: Symbol ‘token’ at (1) has no IMPLICIT type /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:628:53: 628 | cset, corder, f_corder_valid, link_type, token, val_size, & | 1 Error: Symbol ‘token’ at (1) has no IMPLICIT type /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:768:56: 768 | link_type, corder_valid, corder, cset, token, val_size, lapl_id_default) & | 1 Error: Symbol ‘token’ at (1) has no IMPLICIT type /var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:657:56: 657 | cset, corder, corder_valid, link_type, token, val_size, & | 1 Error: Symbol ‘token’ at (1) has no IMPLICIT type Is it the same bug or something different? h5i_invalid_hid_f is never mentioned in the log file.
Building with MAKEOPTS="-j1", the error "symbol has no IMPLICIT type" applies to h5f_libver_error_f, h5f_libver_nbounds_f, h5f_libver_v110_f, h5f_libver_v112_f... and other 11 symbols (at least). All those symbols are defined in fortran/src/H5f90global.F90
Uninstalling the previous version (emerge -C ) before emerging version 1.12.1 worked here.
(In reply to Andreas Proteus from comment #13) > Uninstalling the previous version (emerge -C ) before emerging version > 1.12.1 worked here. it worked for me too
Thus, according to comment #13 and comment #14, h5global.mod from system takes the precedence over the new one; looking at the generated build.ninja, is it possible that -I/usr/include appears too early in the relative INCLUDES?
(In reply to Andreas Proteus from comment #13) > Uninstalling the previous version (emerge -C ) before emerging version > 1.12.1 worked here. Worked here as well.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=225b7ee7e532e58f541e30fbb95d4b193b50236f commit 225b7ee7e532e58f541e30fbb95d4b193b50236f Author: Sam James <sam@gentoo.org> AuthorDate: 2021-10-12 06:51:57 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2021-10-12 06:52:24 +0000 sci-libs/hdf5: workaround build failure with older hdf5 installed Thanks to upstream for the helpful suggestion! Bug: https://github.com/HDFGroup/hdf5/issues/1027 Closes: https://bugs.gentoo.org/808633 Signed-off-by: Sam James <sam@gentoo.org> sci-libs/hdf5/hdf5-1.12.1-r1.ebuild | 4 ++++ 1 file changed, 4 insertions(+)
*** Bug 817920 has been marked as a duplicate of this bug. ***
I am still getting this error on 1.12.2-r1. I was on 1.10 before, but apparently someone removed some '<1.12' or something recently, making this pop up again.
(...) [487/514] /usr/bin/x86_64-pc-linux-gnu-gfortran -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2/fortran/src -I/usr/include -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/h df5-1.12.2/fortran/src -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2_build/bin/shared -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2_build/fortran -I/var/tmp /portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2_build/fortran/src -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2_build/src -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/wor k/hdf5-1.12.2/src -O2 -march=znver3 -pipe -g -ggdb3 -O2 -march=znver3 -pipe -g -ggdb3 -fdiagnostics-urls=never -fno-diagnostics-color -Jbin/shared -fPIC -Waliasing -Wall -Wcharacter-tr uncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -ffree-form -fimplicit-none -std=f2008 -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-const ant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Winteger-division -Wfrontend-loop-interchange -fpreprocessed -o fortran/src/CMakeFiles/hdf5_fortran-shar ed.dir/H5Lff.F90.o -c fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5Lff.F90-pp.f90 FAILED: fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5Lff.F90.o bin/shared/h5l.mod /usr/bin/x86_64-pc-linux-gnu-gfortran -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2/fortran/src -I/usr/include -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2 /fortran/src -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2_build/bin/shared -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2_build/fortran -I/var/tmp/portage/s ci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2_build/fortran/src -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2_build/src -I/var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.1 2.2/src -O2 -march=znver3 -pipe -g -ggdb3 -O2 -march=znver3 -pipe -g -ggdb3 -fdiagnostics-urls=never -fno-diagnostics-color -Jbin/shared -fPIC -Waliasing -Wall -Wcharacter-truncation - Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -ffree-form -fimplicit-none -std=f2008 -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunc tion-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Winteger-division -Wfrontend-loop-interchange -fpreprocessed -o fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5L ff.F90.o -c fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5Lff.F90-pp.f90 /var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2/fortran/src/H5Lff.F90:49:28: 49 | TYPE(H5O_TOKEN_T_F) :: token | 1 Error: Derived type at (1) has not been previously defined and so cannot appear in a derived type definition /var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2/fortran/src/H5Lff.F90:644:24: 644 | TYPE(H5O_TOKEN_T_F), INTENT(OUT), TARGET :: token ! If the link is a hard link, token specifies the object token that the link points to | 1 Error: Derived type ‘h5o_token_t_f’ at (1) is being used before it is defined /var/tmp/portage/sci-libs/hdf5-1.12.2-r1/work/hdf5-1.12.2/fortran/src/H5Lff.F90:660:47: 660 | IMPORT :: HID_T, SIZE_T, H5O_TOKEN_T_F | 1 (...) I was on 1.10.5-r1 to be precise.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7b5147d4ad8bb8149453c743042e87756d5e11e4 commit 7b5147d4ad8bb8149453c743042e87756d5e11e4 Author: Roman Beranek <roman.beranek@prusa3d.com> AuthorDate: 2022-05-31 23:02:59 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2022-05-31 23:43:41 +0000 sci-libs/hdf5: fix cmake include dir regression An attempt to build hdf5-1.12.2-r1 with USE='fortran' on a system where an older version of the package has already been installed will fail due to system headers taking precedence over the ones present in the source directory. This exact issue (#808633) has already been fixed in 225b7ee for 1.12.1, though the workaround somehow hadn't made it into the new ebuild. This commit brings it in. Bug: HDFGroup/hdf5#1027 Closes: https://bugs.gentoo.org/808633 Signed-off-by: Roman Beranek <roman.beranek@prusa3d.com> Closes: https://github.com/gentoo/gentoo/pull/25712 Signed-off-by: Sam James <sam@gentoo.org> sci-libs/hdf5/hdf5-1.12.2-r1.ebuild | 4 ++++ 1 file changed, 4 insertions(+)
