FS#78003 - [hdf5-openmpi-1.14.0-1] build paths present, breaks build deps

Attached to Project: Community Packages
Opened by Jed Brown (jedbrown) - Sunday, 26 March 2023, 16:17 GMT
Last edited by Antonio Rojas (arojas) - Wednesday, 29 March 2023, 07:07 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To No-one
Architecture All
Severity Medium
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

Details

Description:
The installed package contains build paths, which breaks configure and builds for many packages that use hdf5.

Additional info:
hdf5-openmpi-1.14.0-1

Steps to reproduce:
This contains `/build/`
```
$ h5c++ -show
mpicxx -I/build/hdf5-openmpi/src/hdf5-1.14.0/src/H5FDsubfiling -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/hdf5-openmpi/src=/usr/src/debug/hdf5-openmpi -flto=auto -L/usr/lib -lhdf5_hl_cpp -lhdf5_cpp -lhdf5_hl -lhdf5 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto=auto -lsz -lz -ldl -lm -Wl,-rpath -Wl,/usr/lib
```
This task depends upon

Closed by  Antonio Rojas (arojas)
Wednesday, 29 March 2023, 07:07 GMT
Reason for closing:  Fixed
Additional comments about closing:  hdf5-openmpi 1.14.0-3
Comment by Jed Brown (jedbrown) - Tuesday, 28 March 2023, 20:56 GMT
  • Field changed: Percent Complete (100% → 0%)
It is not fixed in hdf5-openmpi-1.14.0-2 because the patch hard-coded /build/hdf5/ when we need /build/hdf5-openmpi/ or more generically, /build/${pkgname}/.
Comment by Antonio Rojas (arojas) - Tuesday, 28 March 2023, 20:56 GMT
Please describe exactly which packages fails to build
Comment by Adrian Insaurralde (adrianinsaval) - Wednesday, 29 March 2023, 01:13 GMT
freecad-git AUR package fails to build:

-- Configuring done (32.3s)
CMake Error in src/3rdParty/salomesmesh/CMakeLists.txt:
Imported target "VTK::hdf5" includes non-existent path

"/build/hdf5-openmpi/src/hdf5-1.14.0/src/H5FDsubfiling"

in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:

* The path was deleted, renamed, or moved to another location.

* An install or uninstall procedure did not complete successfully.

* The installation package was faulty and references files it does not
provide.

find here the full log: https://github.com/adrianinsaval/pacman-repo/actions/runs/4543173994/jobs/8007525196
Comment by Jed Brown (jedbrown) - Wednesday, 29 March 2023, 04:16 GMT
Right, any CMake package will be broken and the h5c++ and h5pcc -show reproducers fail for the same reason because the sed command inherited from hdf5 matched nothing. I thought namcap once did something like the following, but evidently not now. The -I/build/... parts in particular are problematic.

$ unzstd --stdout /var/cache/pacman/pkg/hdf5-openmpi-1.14.0-2-x86_64.pkg.tar.zst | strings | grep /build/
H5BLD_CXXFLAGS=" -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/hdf5-openmpi/src=/usr/src/debug/hdf5-openmpi -flto=auto"
H5BLD_CPPFLAGS=" -I/build/hdf5-openmpi/src/hdf5-1.14.0/src/H5FDsubfiling "
H5BLD_CFLAGS=" -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/hdf5-openmpi/src=/usr/src/debug/hdf5-openmpi -flto=auto"
H5BLD_CPPFLAGS=" -I/build/hdf5-openmpi/src/hdf5-1.14.0/src/H5FDsubfiling "
AM_CPPFLAGS: -I/build/hdf5-openmpi/src/hdf5-1.14.0/src/H5FDsubfiling
C Flags: -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/hdf5-openmpi/src=/usr/src/debug/hdf5-openmpi -flto=auto
C++ Flags: -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/hdf5-openmpi/src=/usr/src/debug/hdf5-openmpi -flto=auto
AM_CPPFLAGS: -I/build/hdf5-openmpi/src/hdf5-1.14.0/src/H5FDsubfiling
C Flags: -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/hdf5-openmpi/src=/usr/src/debug/hdf5-openmpi -flto=auto
C++ Flags: -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/hdf5-openmpi/src=/usr/src/debug/hdf5-openmpi -flto=auto
Comment by Antonio Rojas (arojas) - Wednesday, 29 March 2023, 07:07 GMT
My bad, really fixed now

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