Bug#1002142: shasta: FTBFS: PythonModule.cpp:40:29: error: expected primary-expression before ‘(’ token
Hello, Thank you for the report. I will have a look at whether or not I can reproduce this, and will fix accordingly. Kind regards, Shayan -- Shayan Doust - 201427418 Fingerprint: 0401 A810 A6F2 4303 1EA3 9759 6D7D 4419 19D0 2395 Note: all emails sent by me are signed with my PGP key. signature.asc Description: PGP signature
Bug#982699: Some care for intake package (tests)
Hello, I'm just writing this email as it seems like intake is going to be autoremoved soon, due to a FTBFS [bug]. Unfortunately, due to life events, I am going to be occupied elsewhere for a week or so. If anyone kindly has time to look at this package, please feel free to do so. Just a note that it upstream has in fact released a new version that *should* address the faults. Kind regards, Shayan Doust [bug]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=982699 OpenPGP_0x6D7D441919D02395.asc Description: application/pgp-keys OpenPGP_signature Description: OpenPGP digital signature
Bug#982212: marked as pending in simka
Control: tag -1 pending Hello, Bug #982212 in simka reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/simka/-/commit/3f2bd5ec6aec77dd4e97d9281f8114927d4de765 Make autopkgtest have the same arch list as d/control (Closes: #982212) (this message was generated automatically) -- Greetings https://bugs.debian.org/982212
Bug#971177: intake: FTBFS: TypeError: 'NoneType' object is not iterable
Control: tags -1 help This seems to be a tricky one that I never spotted and just managed to reproduce (although, I do not understand why during my packaging efforts, this error did not occur whereas now it does). It seems like intake, specifically its gui component, relies on [panel], which is not yet packaged. However, panel relies on Bokeh, where if I remember correctly is currently a mess[2] and doesn't seem like any progress has been made. So, I am not too sure what to do here. Kind regards, Shayan Doust [panel]: https://pypi.org/project/panel/ [2]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=756017 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#963392: [Help] Re: r-cran-rstanarm: FTBFS: error: (converted from warning) TBB library not found.
Hello again Andreas, This [commit] now rectifies the build issue for r-cran-prophet. I can build r-cran-prophet successfully after re-building r-cran-rstan with the new patch. Within r-cran-prophet: $ autopkgtest . -- null [TRUNCATED] /usr/bin/ld: cannot find -lStanHeaders collect2: error: ld returned 1 exit status make: *** [/usr/share/R/share/make/shlib.mk:6: sourceCpp_2.so] Error 1 -- 2. Error: (unknown) (@test_stan_functions.R#9) - $ operator is invalid for atomic vectors Backtrace: 1. base::tryCatch(...) 2. base:::tryCatchList(expr, classes, parentenv, handlers) 3. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4. value[[3L]](cond) 5. rstan::expose_stan_functions(...) == testthat results === [ OK: 160 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 2 ] 1. Error: (unknown) (@test_prophet.R#9) 2. Error: (unknown) (@test_stan_functions.R#9) There exists some failed tests, however 160 pass! Kind regards, Shayan Doust [commit]: https://salsa.debian.org/r-pkg-team/r-cran-rstan/-/commit/7351289242ba080c112b1c15784e57f154a79076 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#963392: [Help] Re: r-cran-rstanarm: FTBFS: error: (converted from warning) TBB library not found.
Hello Andreas,
I see the error within r-cran-prophet's build.
It seems like this issue stems from r-cran-rstan (as the call stack shows).
Specifically:
$ grep -r "system.file(\"lib\""
R/plugin.R:RcppParallel_pkg_libs <- system.file("lib", .Platform$r_arch,
R/plugin.R:rstan_StanServices <- system.file("lib", .Platform$r_arch,
"libStanServices.a",
I believe the first line (regarding RcppParallel_pkg_libs) is of concern and the
cause as again, the library location assumption is wrong.
I will write a patch for this too, and I'll test anymore findings.
Kind regards,
Shayan Doust
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Bug#963392: [Help] Re: r-cran-rstanarm: FTBFS: error: (converted from warning) TBB library not found.
Hello Andreas, The [commit] is now pushed for r-cran-rcppparallel, which fixes the "TBB library not found" error thrown for r-cran-rstanarm. Just a note that I did not make it through the entire build process. I gave the build 40 mins before giving up. Compiling r-cran-stanarm used almost all of my 4 GB of RAM on my test server and it resorted to using most of my swap space, so I am unable to test for any other issues. I've left this bug open. Kind regards, Shayan Doust [commit]: https://salsa.debian.org/r-pkg-team/r-cran-rcppparallel/-/commit/e8fcee92d68a420ca1441479661d74add27f519e 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#963392: [Help] Re: r-cran-rstanarm: FTBFS: error: (converted from warning) TBB library not found.
Hello Andreas, Yes, this does seem like a local issue to r-cran-rcppparallel. tbb and variants are loaded when r-cran-rcppparallel is imported, as seen in [hooks.R]. The function of interest is 'tbbLibPath()', which seems to depict tbb library path. With some more investigation, you can see this function within [build.R]. You can see for all supported platforms apart from Windows and Sparc systems, it seems like it expects the library to be situated under lib/ (due to the first argument used within system.file()). I'll try to write a simple patch for this hook file. For a Debian package, this assumption for library location is plain wrong. Kind regards, Shayan Doust [hooks.R]: https://github.com/RcppCore/RcppParallel/blob/b216ba27dcbd3c523932bd918b6dd0b1b08d3566/R/hooks.R#L8 [build.R]: https://github.com/RcppCore/RcppParallel/blob/b216ba27dcbd3c523932bd918b6dd0b1b08d3566/R/build.R#L66 On Tue, 8 Sep 2020 20:32:53 +0200 Andreas Tille wrote: > Control: tags -1 help > > Hi, > > any help why TBB is not found? I think this issue is actually causes by > r-cran-rcppparallel since the code copy of libtbb was removed there - > but it seems to not provide the Debian packaged lib properly. > > Kind regards > > Andreas. > > -- > http://fam-tille.de > > 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#966214: marked as pending in vienna-rna
Control: tag -1 pending Hello, Bug #966214 in vienna-rna reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/vienna-rna/-/commit/daf364342855c34c4e29545b4cadd1993232840a Patch to fix gcc-10 FTBFS (Closes: #966214) (this message was generated automatically) -- Greetings https://bugs.debian.org/966214
Bug#958010: yubikey-personalization: ftbfs with GCC-10
Hello, Any rough timeframe as to when this FTBFS is fixed? Kind regards, Shayan Doust 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#905206: Do you have some spare cycles to have a look at this (Was: profnet is marked for autoremoval from testing)
Hello Andreas, Thanks for the reminder. I have not had the chance to look at this again yet but eager enough to have made it the thing I will look at again now. Kind regards, Shayan Doust
Bug#905206: Do you have some spare cycles to have a look at this (Was: profnet is marked for autoremoval from testing)
Hello Andreas, This is new territory - I have spent some time looking at this and so far I could only reproduce all of what was already mentioned above. I will later go more in-depth and try using mem profiling / debugging and some trial and error to try figure out why this gets a segmentation fault because this issue is really annoying and needs rectifying. Kind regards, Shayan Doust
Bug#927166: libbiod0: not installable in sid
Hello Andreas, Honestly never even heard of Dlang so I thought I'd give this a try. I decided to disect and manually experiment with the Makefile to understand this. The compilation stage works well, and this is failing at the linker stage with symbolic handling of the object files. This also tends to happen with poor linker parameters or just some plain misconfig. I am not sure what the main flag in DFLAGS does, but utilising the main flag on the compiler line in Makefile and not the linker line links the software successfully. I am not sure why a linker would need an extensive set of flags that is the same as the compiler. The only fault I now see with this is that it fails at the dh_install stage, as the debian/tmp file for me is empty. I am not sure why and I am not sure what weighing that main flag had on the linker. I decided to manually run dub and dub test and the library unit test does run successfully. The generated binary in the bin file also seems to invoke without a complaint. Those are my discoveries so far with something I've never touched before. First bug reply so I do apologise if I did violate some reply policy. Best Regards, Shayan Doust On 16/04/2019 10:55, Andreas Tille wrote: > On Mon, Apr 15, 2019 at 09:39:17PM +0200, Ralf Treinen wrote: >> Package: libbiod0 >> Version: 0.2.1-1 >> Severity: serious >> User: trei...@debia.org > ^ > @Ralf: Are you sure there is no typo in one of your scripts? > >> libbiod0 is not installable on amd64 or i386 (the only architectures >> for which this binary package exists) in sid, at least since >> 2018-10-30 : it depends on libphobos2-ldc-shared81 which does >> not exist in sid. > > My guess is that this can be simply solved by a rebuild which > is fixed by a new changelog entry in Git. > > @Matthias: > > When I try to build the current state in Git I get: > > ... > ldc2 -wi -g -relocation-model=pic -unittest -main -Icontrib/undead -L-lz -O0 > -d-debug -link-debuglib contrib/undead/cstream.o contrib/undead/stream.o > contrib/undead/doformat.o contrib/ undead/utf.o contrib/undead/*/*.o > bio/core/sequence.o bio/core/kmer.o bio/core/genotype.o bio/core/tinymap.o > bio/core/base.o bio/core/decompress.o bio/core/call.o bio/core/region.o bio/ > core/bgzf/inputstream.o bio/core/bgzf/constants.o bio/core/bgzf/block.o > bio/core/bgzf/virtualoffset.o bio/core/bgzf/compress.o bio/core/bgzf/chunk.o > bio/core/bgzf/outputstream.o bio/core/ utils/format.o > bio/core/utils/exception.o bio/core/utils/outbuffer.o bio/core/utils/stream.o > bio/core/utils/algo.o bio/core/utils/tmpfile.o bio/core/utils/memoize.o > bio/core/utils/ switchendianness.o bio/core/utils/roundbuf.o > bio/core/utils/zlib.o bio/core/utils/bylinefast.o bio/core/utils/range.o > bio/std/file/fastq.o bio/std/file/fasta.o bio/std/file/fai.o bio/std/ > genotype/maf.o bio/std/genotype/snp.o bio/std/range/splitter.o > bio/std/sff/writer.o bio/std/sff/readrange.o bio/std/sff/index.o > bio/std/sff/reader.o bio/std/sff/read.o bio/std/sff/ constants.o > bio/std/maf/reader.o bio/std/maf/block.o bio/std/maf/parser.o > bio/std/experimental/hts/logger.o bio/std/experimental/hts/pileup.o > bio/std/experimental/hts/bgzf_writer.o bio/std/experimental/hts/reads.o > bio/std/experimental/hts/bgzf.o bio/std/experimental/hts/unpack.o > bio/std/experimental/hts/constants.o bio/std/experimental/hts/hashing.o > bio/std/sff/utils/roundup.o bio/std/hts/iontorrent/flowcall.o > bio/std/hts/iontorrent/flowindex.o bio/std/hts/sam/reader.o > bio/std/hts/sam/header.o bio/std/hts/snpcallers/maq.o > bio/std/hts/snpcallers/simple.o bio/ std/hts/bam/abstractreader.o > bio/std/hts/bam/randomaccessmanager.o bio/std/hts/bam/baifile.o > bio/std/hts/bam/writer.o bio/std/hts/bam/pileup.o bio/std/hts/bam/splitter.o > bio/std/hts/bam/ tagvalue.o bio/std/hts/bam/constants.o > bio/std/hts/bam/reference.o bio/std/hts/bam/baseinfo.o > bio/std/hts/bam/readrange.o bio/std/hts/bam/referenceinfo.o > bio/std/hts/bam/multireader.o bio/ std/hts/bam/reader.o > bio/std/hts/bam/read.o bio/std/hts/bam/cigar.o bio/std/hts/bam/region.o > bio/std/hts/thirdparty/msgpack.o bio/std/hts/utils/array.o > bio/std/hts/utils/value.o bio/std/ hts/utils/samheadermerger.o > bio/std/hts/utils/graph.o bio/std/experimental/hts/bam/reader.o > bio/std/experimental/hts/bam/writer.o bio/std/experimental/hts/bam/header.o > bio/std/hts/sam/ utils/recordparser.o > bio/std/hts/sam/utils/fastrecordparser.o bio/std/hts/bam/md/core.o > bio/std/hts/bam/md/operation.o bio/std/hts/bam/md/reconstruct.o > bio/std/hts/bam/md/parse.o bio/std/ hts/bam/bai/bin.o > bio/std/hts/bam/bai/indexing.o bio/std/hts/bam/validation/alignment.o > bio/std/hts/bam/validation/samhea
