Re: sra-sdk: drop B-D on markdown
Pierre Gruet writes: > Ah you're right. And indeed, the build goes smoothly without the line. It may well be a relic of the 2.x days; the build system changed extensively since then. > I offer to remove the whole line in experimental and in unstable, and > will do so within a few days if no concern is raised. Go for it, thanks! -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
Re: Help requested: r-bioc-rhdf5lib patches need updating for bioc-3.19 upgrade
On Wed, Jul 10, 2024 at 06:03:26PM +0200, Michael R. Crusoe wrote:
>
>
> On 10/07/2024 15.58, Nilesh Patra wrote:
> > On Wed, Jul 10, 2024 at 12:14:05PM +0200, Michael R. Crusoe wrote:
> > > I upgraded r-bioc-rhdf5lib from 1.24.2 to 1.26.0 in the
> > > "debian/experimental" branch on salsa.
> > >
> > > https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/tree/debian/experimental?ref_type=heads
> > >
> > > However when I try to build other packages using the resulting
> > > "r-bioc-rhd5lib" binary package, I get the following build errors:
> > >
> > > # From r-bioc-alabaster.base
> > > https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base
> > > g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o
> > > alabaster.base.so RcppExports.o check_csv.o check_list.o
> > > choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o
> > > validate.o /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a
> > > /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a -lcrypto -lcurl -lpthread
> > > -lsz -lz -ldl -lm -lz -L/usr/lib/R/lib -lR
> > > /usr/bin/ld: cannot find
> > > /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a: No such file or
> > > directory
> > > /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a:
> > > No such file or directory
> > > collect2: error: ld returned 1 exit status
> > >
> > > Can I get some help with this?
> > >
> > > Please push any fixes directly to the "debian/experimental" branch on
> > > Salsa and let me know, thank you!
> >
> > I don't have the time to write a patch/hack around this right now, but I
> > understood what the issue is and it should be relatively easy to fix.
> >
> > alabaster.base used Rhdf5lib::pkgconfig("PKG_CXX_LIBS") to get the linker
> > flags
> > for Rhdf5 lib as can be see here[1]
> >
> > This has been set to an incorrect value as per the debian installed
> > package[2].
> > It points to a path that does not exist since we are using hdf5 packaged in
> > debian instead of building and using embedded copies.
> >
> > Patching the code to point to the correct path should fix the issue for you.
>
> Thank you, Nilesh, that got me further!
>
> With
> https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/commit/1ce8837d34d244f60b4a26469ba378babcb0
> I get
>
> g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so
> RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o
> is_rfc3339.o load_csv.o load_list.o validate.o
> /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a
> /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.a -lcrypto -lcurl -lpthread
> -lsz -lz -ldl -lm -lz -L/usr/lib/R/lib -lR
> /usr/bin/ld:
> /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a(H5Exception.o): warning:
> relocation against `_ZTVN2H518DataTypeIExceptionE' in read-only section
> `.text'
> /usr/bin/ld:
> /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a(H5Exception.o):
> relocation R_X86_64_PC32 against symbol `_ZTVN2H59ExceptionE' can not be used
> when making a shared object; recompile with -fPIC
> /usr/bin/ld: final link failed: bad value
> collect2: error: ld returned 1 exit status
> make[1]: *** [/usr/share/R/share/make/shlib.mk:10: alabaster.base.so] Error 1
Probably some hdf5 hackery at play here. On re-looking at it, I wonder if
itmakes sense to pass in
the paths to libhdf5.a -- maybe not from debian pov? We could likely just rely
on -lhdf5.
This patch gets alabaster.base building for me:
--- a/src/Makevars
+++ b/src/Makevars
@@ -1,3 +1,3 @@
-RHDF5_LIBS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e
'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")')
-PKG_CPPFLAGS=-I../inst/include
-PKG_LIBS=$(RHDF5_LIBS) -lz
+RHDF5_LIBS=/usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so
-L/usr/lib/$(shell dpkg-architecture -qDEB_HOST_MULTIARCH)/hdf5/serial -lhdf5
-lhdf5_cpp -lcrypto -lcurl -lpthread -lsz
+PKG_CPPFLAGS=-I../inst/include -I/usr/include/hdf5/serial/
+PKG_LIBS=-fPIC $(RHDF5_LIBS) -lz
Best,
Nilesh
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Re: Help requested: r-bioc-rhdf5lib patches need updating for bioc-3.19 upgrade
On 10/07/2024 15.58, Nilesh Patra wrote:
On Wed, Jul 10, 2024 at 12:14:05PM +0200, Michael R. Crusoe wrote:
I upgraded r-bioc-rhdf5lib from 1.24.2 to 1.26.0 in the "debian/experimental"
branch on salsa.
https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/tree/debian/experimental?ref_type=heads
However when I try to build other packages using the resulting "r-bioc-rhd5lib"
binary package, I get the following build errors:
# From r-bioc-alabaster.base
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so
RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o
is_rfc3339.o load_csv.o load_list.o validate.o
/usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a
/usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a -lcrypto -lcurl -lpthread -lsz
-lz -ldl -lm -lz -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a:
No such file or directory
/usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a: No
such file or directory
collect2: error: ld returned 1 exit status
Can I get some help with this?
Please push any fixes directly to the "debian/experimental" branch on Salsa and
let me know, thank you!
I don't have the time to write a patch/hack around this right now, but I
understood what the issue is and it should be relatively easy to fix.
alabaster.base used Rhdf5lib::pkgconfig("PKG_CXX_LIBS") to get the linker flags
for Rhdf5 lib as can be see here[1]
This has been set to an incorrect value as per the debian installed package[2].
It points to a path that does not exist since we are using hdf5 packaged in
debian instead of building and using embedded copies.
Patching the code to point to the correct path should fix the issue for you.
Thank you, Nilesh, that got me further!
With
https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/commit/1ce8837d34d244f60b4a26469ba378babcb0
I get
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so
RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o
is_rfc3339.o load_csv.o load_list.o validate.o
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.a -lcrypto -lcurl -lpthread -lsz
-lz -ldl -lm -lz -L/usr/lib/R/lib -lR
/usr/bin/ld:
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a(H5Exception.o): warning:
relocation against `_ZTVN2H518DataTypeIExceptionE' in read-only section `.text'
/usr/bin/ld:
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a(H5Exception.o): relocation
R_X86_64_PC32 against symbol `_ZTVN2H59ExceptionE' can not be used when making
a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make[1]: *** [/usr/share/R/share/make/shlib.mk:10: alabaster.base.so] Error 1
For building r-bioc-alabaster.base, feel free to use the bioc-3.19 test
packages I've been making: https://people.debian.org/~crusoe/bioc/
--
Michael R. Crusoe
[1]:
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base/-/blob/master/src/Makevars?ref_type=heads#L1
[2]:
https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/blob/debian/experimental/R/zzz.R?ref_type=heads#L73
Best,
Nilesh
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Re: Help requested: r-bioc-rhdf5lib patches need updating for bioc-3.19 upgrade
On Wed, Jul 10, 2024 at 12:14:05PM +0200, Michael R. Crusoe wrote:
> I upgraded r-bioc-rhdf5lib from 1.24.2 to 1.26.0 in the "debian/experimental"
> branch on salsa.
>
> https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/tree/debian/experimental?ref_type=heads
>
> However when I try to build other packages using the resulting
> "r-bioc-rhd5lib" binary package, I get the following build errors:
>
> # From r-bioc-alabaster.base
> https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base
> g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so
> RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o
> is_rfc3339.o load_csv.o load_list.o validate.o
> /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a
> /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a -lcrypto -lcurl -lpthread
> -lsz -lz -ldl -lm -lz -L/usr/lib/R/lib -lR
> /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a:
> No such file or directory
> /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a: No
> such file or directory
> collect2: error: ld returned 1 exit status
>
> Can I get some help with this?
>
> Please push any fixes directly to the "debian/experimental" branch on Salsa
> and let me know, thank you!
I don't have the time to write a patch/hack around this right now, but I
understood what the issue is and it should be relatively easy to fix.
alabaster.base used Rhdf5lib::pkgconfig("PKG_CXX_LIBS") to get the linker flags
for Rhdf5 lib as can be see here[1]
This has been set to an incorrect value as per the debian installed package[2].
It points to a path that does not exist since we are using hdf5 packaged in
debian instead of building and using embedded copies.
Patching the code to point to the correct path should fix the issue for you.
> For building r-bioc-alabaster.base, feel free to use the bioc-3.19 test
> packages I've been making: https://people.debian.org/~crusoe/bioc/
>
> --
> Michael R. Crusoe
[1]:
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base/-/blob/master/src/Makevars?ref_type=heads#L1
[2]:
https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/blob/debian/experimental/R/zzz.R?ref_type=heads#L73
Best,
Nilesh
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Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
Hi again, Étienne Mollier, on 2024-07-10: > Full log would probably be better suited in your issue tracker > than in a mailing list. Let me know if you need it. I tried to > trip Salsa CI so it produces an independent build and a build > log to point to, but it doesn't look to be operating right now. Actually, the CI kicked in and reported a different set of test failures[1]. I'm not sure what's up. Does this ring a bell? [1]: https://salsa.debian.org/med-team/bali-phy/-/jobs/5952519 Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/0, please excuse my verbosity `-on air: Saga - (Goodbye) Once Upon A Time signature.asc Description: PGP signature
Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
Hi Benjamin, On 6/20/24 11:16 PM, Benjamin Redelings wrote: > Thanks a lot from me as well! I see the 4.0-beta13 version in > experimental now. > > I noticed that some of the tests for 4.0-beta13 passed, but some timed > out.: > > https://salsa.debian.org/med-team/bali-phy/-/jobs/5786155 > > I have released a 4.0-beta14 that decreases startup times, so that the > tests run more quickly. Hopefully this will prevent timeouts in future > packaged versions. Thanks for revising the test suite to get tests to pass in a reasonable timespan; sorry it took me some time to get to it as I had busy schedule in the past few weeks. I ran the test suite during the build on 4.0-beta14 and caught a few failures: Summary of Failures: 33/37 bali-phy 48 +A 3 FAIL 0.33s exit status 1 34/37 bali-phy 5d -A 200 FAIL 0.33s exit status 1 35/37 bali-phy 5d +A 50 FAIL 0.55s exit status 1 37/37 bali-phy testsuite FAIL 28.58s exit status 1 Ok: 33 Expected Fail: 0 Fail: 4 Unexpected Pass:0 Skipped:0 Timeout:0 Here are the detailed test output for 33, 34 and 35: === 33/37 test: bali-phy 48 +A 3 start time: 10:07:08 duration: 0.33s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=37 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 '/<>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<>/obj-x86_64-linux-gnu/../examples/5S-rRNA/48-muscle.fasta' --iter=3 '--package-path=/<>/obj-x86_64-linux-gnu/src/builtins:/<>' --- stderr --- Created directory "48-muscle-1" for output files. bali-phy: Error! In module 'Text.Show': Can't add alias 'Data.List.dmelem_11304' -> 'Data.Foldable.dmelem_11304' in module 'Text.Show' because 'Data.Foldable.dmelem_11304' is neither declared nor imported. == === 34/37 test: bali-phy 5d -A 200 start time: 10:07:08 duration: 0.33s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=228 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 '/<>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<>/obj-x86_64-linux-gnu/../examples/5S-rRNA/5d-muscle.fasta' --iter=200 '--package-path=/<>/obj-x86_64-linux-gnu/src/builtins:/<>' -Inone --- stderr --- Created directory "5d-muscle-2" for output files. bali-phy: Error! In module 'Text.Show': Can't add alias 'Data.List.dmelem_11304' -> 'Data.Foldable.dmelem_11304' in module 'Text.Show' because 'Data.Foldable.dmelem_11304' is neither declared nor imported. == === 35/37 test: bali-phy 5d +A 50 start time: 10:07:08 duration: 0.55s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=173 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 '/<>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<>/obj-x86_64-linux-gnu/../examples/5S-rRNA/5d-muscle.fasta' --iter=50 '--package-path=/<>/obj-x86_64-linux-gnu/src/builtins:/<>' --- stderr --- Created directory "5d-muscle-1" for output files. bali-phy: Error! In module 'Bio.Alignment.Class': Can't add alias 'Prelude.dmenumFromThenTo_3345' -> 'Compiler.Enum.dmenumFromThenTo_3345' in module
Re: sra-sdk: drop B-D on markdown
Hi Charles, Le 08/07/2024 à 03:52, Charles Plessy a écrit : Le Sat, Jul 06, 2024 at 03:54:21PM +0200, Pierre Gruet a écrit : As this B-D has alternatives (markdown | libtext-markdown-perl | discount), we should just remove markdown from the alternatives to prevent sra-sdk and its rdeps from being removed. Actually, I wonder if the whole line can just be reomved... I do not see anything in the package that uses the markdown command to build documentation. Ah you're right. And indeed, the build goes smoothly without the line. I offer to remove the whole line in experimental and in unstable, and will do so within a few days if no concern is raised. Have a nice day, Charles Same to you, -- Pierre OpenPGP_signature.asc Description: OpenPGP digital signature
Help requested: r-bioc-rhdf5lib patches need updating for bioc-3.19 upgrade
[whoops, forgot to include the debian-r list] Hello teams, I upgraded r-bioc-rhdf5lib from 1.24.2 to 1.26.0 in the "debian/experimental" branch on salsa. https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/tree/debian/experimental?ref_type=heads However when I try to build other packages using the resulting "r-bioc-rhd5lib" binary package, I get the following build errors: # From r-bioc-alabaster.base https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -lz -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a: No such file or directory /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a: No such file or directory collect2: error: ld returned 1 exit status Can I get some help with this? Please push any fixes directly to the "debian/experimental" branch on Salsa and let me know, thank you! For building r-bioc-alabaster.base, feel free to use the bioc-3.19 test packages I've been making: https://people.debian.org/~crusoe/bioc/ -- Michael R. Crusoe OpenPGP_signature.asc Description: OpenPGP digital signature
Help requested: r-bioc-rhdf5lib patches need updating for bioc-3.19 upgrade
Hello team, I upgraded r-bioc-rhdf5lib from 1.24.2 to 1.26.0 in the "debian/experimental" branch on salsa. https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/tree/debian/experimental?ref_type=heads However when I try to build other packages using the resulting "r-bioc-rhd5lib" binary package, I get the following build errors: # From r-bioc-alabaster.base https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -lz -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a: No such file or directory /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a: No such file or directory collect2: error: ld returned 1 exit status Can I get some help with this? Please push any fixes directly to the "debian/experimental" branch on Salsa and let me know, thank you! For building r-bioc-alabaster.base, feel free to use the bioc-3.19 test packages I've been making: https://people.debian.org/~crusoe/bioc/ -- Michael R. Crusoe OpenPGP_signature.asc Description: OpenPGP digital signature
