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#69254 closed defect (fixed)

hdf5: recent update has broken destroot

Reported by:	barracuda156	Owned by:	eborisch (Eric A. Borisch)
Priority:	Normal	Milestone:
Component:	ports	Version:	2.9.0
Keywords:		Cc:	Michael-P-Allen (Mike Allen), Dave-Allured (Dave Allured), scrallen
Port:	hdf5

Description

:debug:destroot Executing proc-post-org.macports.destroot-destroot-0
:debug:destroot Executing proc-post-org.macports.destroot-destroot-1
:info:destroot xinstall: mkdir /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/share/hdf5
:info:destroot xinstall: /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.3/COPYING -> /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/share/hdf5//COPYING
:debug:destroot system -W /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/bin: /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.3/bin/pkgscrpts/h5rmflags -prefix=/opt/local
:info:destroot Update the following tools because they are now installed at a new directory
:info:destroot h5pcc:
:info:destroot    current setting="/opt/local"
:info:destroot    new     setting="/opt/local"
:info:destroot h5pfc:
:info:destroot    current setting="/opt/local"
:info:destroot    new     setting="/opt/local"
:info:destroot h5c++:
:info:destroot    current setting="/opt/local"
:info:destroot    new     setting="/opt/local"
:info:destroot Update h5pcc ...
:info:destroot H5BLD_LDFLAGS=" -lMacportsLegacySupport "
:info:destroot Update h5pfc ...
:info:destroot H5BLD_LDFLAGS=" -lMacportsLegacySupport "
:info:destroot Update h5c++ ...
:info:destroot H5BLD_LDFLAGS=" -lMacportsLegacySupport "
:info:destroot --->  Patching h5c++: s|-lsz|/opt/local/lib/libaec/lib/libsz.dylib|g
:debug:destroot Executing reinplace: /usr/bin/sed s|-lsz|/opt/local/lib/libaec/lib/libsz.dylib|g </opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/bin/h5c++ >@file17
:info:destroot --->  Patching h5pcc: s|-lsz|/opt/local/lib/libaec/lib/libsz.dylib|g
:debug:destroot Executing reinplace: /usr/bin/sed s|-lsz|/opt/local/lib/libaec/lib/libsz.dylib|g </opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/bin/h5pcc >@file17
:info:destroot --->  Patching h5fc: s|-lsz|/opt/local/lib/libaec/lib/libsz.dylib|g
:debug:destroot Executing reinplace: /usr/bin/sed s|-lsz|/opt/local/lib/libaec/lib/libsz.dylib|g </opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/bin/h5fc >@file17
:debug:destroot couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/bin/h5fc": no such file or directory
:debug:destroot     while executing
:debug:destroot "exec -ignorestderr -- {*}$cmdline"
:error:destroot reinplace: couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/bin/h5fc": no such file or directory
:error:destroot Failed to destroot hdf5: reinplace sed(1) failed
:debug:destroot Error code: NONE
:debug:destroot Backtrace: reinplace sed(1) failed
:debug:destroot     while executing
:debug:destroot "$post $targetname"

Attachments (1)

hdf5.log (8.6 MB) - added by barracuda156 3 months ago.

Change History (12)

comment:1 Changed 4 months ago by Michael-P-Allen (Mike Allen)

Cc:	Michael-P-Allen added

comment:2 Changed 4 months ago by eborisch (Eric A. Borisch)

This must have been a non Fortran variant build. (Build bots succeeded with defaults.)

Will fix when I have a moment.

comment:3 follow-ups: 4 5 Changed 4 months ago by Eric A. Borisch <eborisch@…>

Resolution:	→ fixed
Status:	assigned → closed

In b084614a56ed9b3108917fbb4a2db428d5e26fba/macports-ports (master):

hdf5: Only patch h5fc on +fortran. (https://github.com/macports/macports-ports/pull/22510)

Fixes: #69254

comment:4 in reply to: 3 Changed 3 months ago by barracuda156

Replying to Eric A. Borisch <eborisch@…>:

In b084614a56ed9b3108917fbb4a2db428d5e26fba/macports-ports (master):

hdf5: Only patch h5fc on +fortran. (https://github.com/macports/macports-ports/pull/22510)

Fixes: #69254

Unfortunately, nothing changed.

I am installing hdf5 @1.14.3_3+cxx+fortran+gcc13+hl+mpich. Gonna attach the log now (it has two attempts, on Feb 1 and now).

Changed 3 months ago by barracuda156

Attachment:	hdf5.log added

comment:5 in reply to: 3 Changed 3 months ago by barracuda156

Replying to Eric A. Borisch <eborisch@…>:

Here is what sitting in destroot in bin:

h5c++
h5clear
h5copy
h5debug
h5delete
h5diff
h5dump
h5format_convert
h5fuse.sh
h5import
h5jam
h5ls
h5mkgrp
h5pcc
h5perf
h5perf_serial
h5pfc
h5redeploy
h5repack
h5repart
h5stat
h5tools_test_utils
h5unjam
h5watch
ph5diff

comment:6 follow-up: 8 Changed 3 months ago by Eric A. Borisch <eborisch@…>

In f0e6d3ac6bb521f5a3810fc49933d44b45974fca/macports-ports (master):

hdf5: Another attempt at fixing wrapper scripts (https://github.com/macports/macports-ports/pull/22559)

A number of wrapper scripts need to have their -lsz -lz link line
fixed; which ones depends on build config. Rather than have a matrix of
all the different potential files that need patching, just find them at
build time and fix them up.

Another attempt at:

Fixes #69254

comment:7 Changed 3 months ago by Dave-Allured (Dave Allured)

Cc:	Dave-Allured added

comment:8 in reply to: 6 Changed 3 months ago by barracuda156

Replying to Eric A. Borisch <eborisch@…>:

In f0e6d3ac6bb521f5a3810fc49933d44b45974fca/macports-ports (master):

hdf5: Another attempt at fixing wrapper scripts (https://github.com/macports/macports-ports/pull/22559)

A number of wrapper scripts need to have their -lsz -lz link line
fixed; which ones depends on build config. Rather than have a matrix of
all the different potential files that need patching, just find them at
build time and fix them up.

Another attempt at:

Fixes #69254

This update still fails, but differently: https://github.com/macports/macports-ports/pull/22559#issuecomment-1928098050 Now there is some issue with sed syntax:

:debug:destroot Executing proc-post-org.macports.destroot-destroot-0
:debug:destroot Executing proc-post-org.macports.destroot-destroot-1
:info:destroot xinstall: mkdir /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/share/hdf5
:info:destroot xinstall: /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.3/COPYING -> /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/share/hdf5//COPYING
:debug:destroot system -W /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/bin: /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.3/bin/pkgscrpts/h5rmflags -prefix=/opt/local
:info:destroot Update the following tools because they are now installed at a new directory
:info:destroot h5pcc:
:info:destroot    current setting="/opt/local"
:info:destroot    new     setting="/opt/local"
:info:destroot h5pfc:
:info:destroot    current setting="/opt/local"
:info:destroot    new     setting="/opt/local"
:info:destroot h5c++:
:info:destroot    current setting="/opt/local"
:info:destroot    new     setting="/opt/local"
:info:destroot Update h5pcc ...
:info:destroot H5BLD_LDFLAGS=" -lMacportsLegacySupport "
:info:destroot Update h5pfc ...
:info:destroot H5BLD_LDFLAGS=" -lMacportsLegacySupport "
:info:destroot Update h5c++ ...
:info:destroot H5BLD_LDFLAGS=" -lMacportsLegacySupport "
:debug:destroot system -W /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/destroot/opt/local/bin: grep -Il --null -- '-lsz -lz' * | xargs -0 sed -I ''  -e 's^-lsz^/opt/local/lib/libaec/lib/libsz.dylib^'  -e 's^-lz^/opt/local/lib/libz.dylib^'
:info:destroot sed: illegal option -- I
:info:destroot usage: sed script [-Ealn] [-i extension] [file ...]
:info:destroot        sed [-Ealn] [-i extension] [-e script] ... [-f script_file] ... [file ...]
:info:destroot Command failed: grep -Il --null -- '-lsz -lz' * | xargs -0 sed -I ''  -e 's^-lsz^/opt/local/lib/libaec/lib/libsz.dylib^'  -e 's^-lz^/opt/local/lib/libz.dylib^'
:info:destroot Exit code: 1
:error:destroot Failed to destroot hdf5: command execution failed
:debug:destroot Error code: NONE

comment:9 follow-up: 10 Changed 3 months ago by Eric A. Borisch <eborisch@…>

In 20cd298d83d8886aad95afcabced77c993055249/macports-ports (master):

hdf5: Remove old sed flag.

Make work with older sed. Not bumping (completed builds won't change result).

Once more hopefully fixes: #69254

comment:10 in reply to: 9 Changed 3 months ago by barracuda156

Replying to Eric A. Borisch <eborisch@…>:

In 20cd298d83d8886aad95afcabced77c993055249/macports-ports (master):

hdf5: Remove old sed flag.

Make work with older sed. Not bumping (completed builds won't change result).

Once more hopefully fixes: #69254

Thanks, will try soon.

S. Sorry, I understand it is annoying to have to do multiple iterations, but I could see this problem only after the previous one was fixed.

comment:11 Changed 3 months ago by scrallen

Cc:	scrallen added

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