Bug#1064135: bigmemory: fails to migrate to testing for too long: autopkgtest fails on arm*, ppc64el and s390x

2025-05-07 Thread Charles Plessy
On Wed, 7 May 2025 18:11:57 +0900 Charles Plessy wrote: > Hi all, > > I am trying to pass -fsigned-char to the compiler when building the > package but failed to do it by adding a src/Makevars file. (see patch > below). What is the standard approach? > --- /dev/null >

Bug#1064135: bigmemory: fails to migrate to testing for too long: autopkgtest fails on arm*, ppc64el and s390x

2025-05-07 Thread Charles Plessy
l run on MacOS. In Debian, r-cran-bigmemory fails on arm64 and a lot of other architectures. In my understanding, char is signed on macos-arm64 and linux amd64 (x86_64) and unsigned on linux arm64. This patch passes -fsigned-char to the compiler. Author: Charles Plessy Bug-Debian:

Bug#1100292: Debian packaged Fastcluster fails its test (Was: r-cran-fastcluster: FTBFS: FAIL: test_vector (tests.fastcluster_test.test_vector))

2025-05-02 Thread Charles Plessy
than two weeks we will have remove fastcluster from the next Debian release, and all the packages that depend on it, if we have reasons to worry that the package is not fit for the release. How bad are is test failure? Is that something that can be ignored? Have a nice day, Charles -- Charles

Bug#1064135: bigmemory: fails to migrate to testing for too long: autopkgtest fails on arm*, ppc64el and s390x

2025-05-02 Thread Charles Plessy
er architectures. In my understanding, `char` is signed on `macos-arm64` and linux `amd64` (`x86_64`) and unsigned on linux `arm64`. Would it solve the problem if _bigmemory_ would pass `-fsigned-char` to the compilers? Cheers, Charles -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@o

Bug#1102447: marked as pending in r-cran-rtf

2025-05-01 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1102447 in r-cran-rtf 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/r-pkg-team/r-cran-rtf/-/commit/79b169f0b6d738793bc1a2f

Bug#1104495: [R-pkg-team] Bug#1104495: r-cran-httr2: flaky tests on riscv64

2025-05-01 Thread Charles Plessy
; Please ensure the tests are stable enough for automated testing, on all > archs. > > Thanks, > Chris > > ___ > R-pkg-team mailing list > r-pkg-t...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailma

Bug#1104193: pv-grub-menu: Should pv-grub-menu be removed from unstable?

2025-04-26 Thread Charles Plessy
Thanks Andreas, on my side I agree with the removal. Have a nice Sunday, Charles Le Sun, Apr 27, 2025 at 08:09:05AM +0200, Andreas Tille a écrit : > Source: pv-grub-menu > Version: 1.3+nmu1 > Severity: serious > Justification: grab attention of maintainer > X-Debbugs-Cc:

Bug#1099927: [R-pkg-team] Bug#1099927: r-cran-testthat does not actually break other packages

2025-04-22 Thread Charles Plessy
ease let me know if there is a better way. Cheers, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med Tooting from home https://framapiaf.org/@charles_plessy - You do no

Bug#1102590: [R-pkg-team] Bug#1102590: r-cran-fansi fails to migrate to testing

2025-04-22 Thread Charles Plessy
an-fansi stays at version 1.0.5-1 in Trixie. But won't it prevent 4.5.0-2 from migrating? Have a nice day, Charles -- Charles Plessy http://charles.plessy.org Nagahama, Yomitan, Okinawa, Japan

Bug#1103201: RM: r-cran-genabel, r-cran-genabel.data -- RoM; RC-buggy, abandonned upstream

2025-04-20 Thread Charles Plessy
remove r-cran-genabel.data. Thanks! Charles Le Wed, Apr 16, 2025 at 04:29:17PM +0900, Charles Plessy a écrit : > Thanks a lot but maybe we just should remove r-cran-genabel altogether? > > https://cran.r-project.org/web/packages/GenABEL/index.html > > Have a nice day, > >

Bug#1102590: r-cran-fansi fixed, not yet uploaded.

2025-04-18 Thread Charles Plessy
I am far from my key. Given the flood of autoremoval messages today, please feel free to upload the package before I am back home! Have a nice week-end, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org

Bug#1103227: marked as pending in r-bioc-grohmm

2025-04-17 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1103227 in r-bioc-grohmm 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/r-pkg-team/r-bioc-grohmm/-/commit/4054e62028b49ba19

Bug#1103227: [R-pkg-team] Bug#1103227: [reply ] r-bioc-grohmm: FTBFS: DecayAlgorithm.c:94:15: error: expected identifier or '(' before 'false'

2025-04-16 Thread Charles Plessy
ts it belongs to BioC 3.21 and intentionally adds a virtual dependency that prevents the package from co-existing with BioC 3.20 packages. It's easy to workaround with a patch, but in that case patching the current version in Debian is as easy and more conservative. Cheers, Charles -- Charles Ples

Bug#1103199: [R-pkg-team] Bug#1103199: Bug#1103199: [PATCH] Fix for FTBFS with R 4.5.0

2025-04-16 Thread Charles Plessy
Le Wed, Apr 16, 2025 at 05:21:59PM +0900, Charles Plessy a écrit : > > Instead of carrying a patch, I would like to propose to upgrade to the new > upstream version that will be released very soon. Hi again, I tested an upgrade locally, but it gets convoluted with the Bioconductor t

Bug#1103199: [R-pkg-team] Bug#1103199: [PATCH] Fix for FTBFS with R 4.5.0

2025-04-16 Thread Charles Plessy
Thanks again liwenjun for the patch, I just had a look at the upstream GitHub repository and it is probably fixed there. https://github.com/benilton/oligo/commits/devel/ Instead of carrying a patch, I would like to propose to upgrade to the new upstream version that will be released very soon.

Bug#1103201: [R-pkg-team] Bug#1103201: [PATCH] Fix for FTBFS with R 4.5.0

2025-04-16 Thread Charles Plessy
; > > @@ -302,7 +302,7 @@ fexact(int *nrow, int *ncol, int *table, > dwrk + irwk); > > > - Free(equiv); > + R_Free(equiv); > > return; > } > ___ > R-pkg-team mailing list > r-

Bug#1100292: r-cran-fastcluster: FTBFS: FAIL: test_vector (tests.fastcluster_test.test_vector)

2025-04-10 Thread Charles Plessy
, ..., 0.42857143, 0., 0.]], shape=(62, 62))) ---------- Ran 3 tests in 1.095s == -- Charle

Bug#1102548: [R-pkg-team] Bug#1102548: r-cran-dendextend: autopkgtest failure

2025-04-10 Thread Charles Plessy
that. Have a nice day, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med Tooting from work, https://fediscience.org/@charles_plessy Tooting from home, https

Bug#1071104: marked as pending in r-cran-performance

2025-04-09 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1071104 in r-cran-performance 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/r-pkg-team/r-cran-performance/-/commit/8b44e48

Bug#1071104: [R-pkg-team] Bug#1071104: r-cran-performance: diff for NMU version 0.13.0-2.1

2025-04-09 Thread Charles Plessy
Le Thu, Apr 10, 2025 at 02:03:52AM +0300, Adrian Bunk a écrit : > > I've prepared an NMU for r-cran-performance (versioned as 0.13.0-2.1) > and uploaded it to DELAYED/1. Please feel free to tell me if I should > cancel it. Thanks a lot Adrian, since we strongly prefer team uploads pushed on Sa

Bug#1101729: 1101729

2025-04-09 Thread Charles Plessy
oves the need for sed. Have a nice day, Charles -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp Okinawa Institute of Science and Technology Graduate University Senior staff scientist ~~ Luscombe Unit ~~ https://groups.oist.jp/grsu Toots from work - ~~ ~~~

Bug#1102447: r-cran-rtf: autopkgtest failure

2025-04-09 Thread Charles Plessy
Le Wed, Apr 09, 2025 at 10:44:52AM +0300, Adrian Bunk a écrit : > > Issues preventing migration: > ∙ ∙ autopkgtest for r-cran-rtf/0.4-14.1-2: amd64: Regression or new test ♻, > arm64: Regression or new test ♻, armel: Regression or new test ♻, armhf: > Regression or new test ♻, i386: Regression

Bug#1101251: marked as pending in r-bioconductor-lpsymphony

2025-04-06 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1101251 in r-bioconductor-lpsymphony 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/r-pkg-team/r-bioc-lpsymphony/-/commit/4

Bug#1101711: marked as pending in r-bioc-ihw

2025-04-06 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1101711 in r-bioc-ihw 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/r-pkg-team/r-bioc-ihw/-/commit/e61e8f103843b99ff2bd867

Bug#1101591: [R-pkg-team] Bug#1101591: r-cran-waveslim: FTBFS: build-dependency not installable: r-cran-multitaper

2025-03-31 Thread Charles Plessy
Thanks Lucas, I have to apologise for this one, I forgot to upload r-cran-multitaper to NEW two weeks ago… Bonne journée ! Charles Le Sat, Mar 29, 2025 at 09:20:09PM +0100, Lucas Nussbaum a écrit : Source: r-cran-waveslim Version: 1.8.5-1 Severity: serious Justification: FTBFS Tags: trixie si

Bug#1092364: [Debian-med-packaging] Bug#1092364: cluster3: needs rebuild for Python 3.13 as default

2025-01-07 Thread Charles Plessy
e day, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med Tooting from home https://framapiaf.org/@charles_plessy - You do not have my permission to use this email to train an AI -

Bug#1072630: r-cran-dplyr needs some love

2024-12-07 Thread Charles Plessy
that disables the test suite. Have a nice week-end, Charles Le Sun, Nov 24, 2024 at 08:44:04AM +0900, Charles Plessy a écrit : > Hi Dirk and everybody, > > yes it is in the radar. I will disable the tests before the removal if I > or others can not fix the failure: > &g

Bug#1072630: Help needed on providing the en_US locale in autopkgtests

2024-11-05 Thread Charles Plessy
vide the needed locale to debci, please let me know. Have a nice day, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian R packaging team https://wiki.debian.org/Teams/r-pkg-team Tooting from home https://framapiaf.org/@charles_pless

Bug#1081117: (r-cran-)survey not migrating to testing autoremovals

2024-10-18 Thread Charles Plessy
4 at 04:14:48PM +0900, Charles Plessy a écrit : > > quick message to say that r-cran-survey now passes all the CI tests > after I converted it to an architecture-dependent package.

Bug#1077454: [Debian-med-packaging] Bug#1077454: bioperl-run: t/SABlastPlus.t failure

2024-07-31 Thread Charles Plessy
ink that it is probably fine to release without it and to consider removing package go if we do not get complains. Have a nice day, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med

Bug#1077463: Forwarded upstream Bug#1077463: r-cran-backports: autopkgtest regression: Testing test_dotlibPaths.R

2024-07-29 Thread Charles Plessy
Control: forwarded 1077463 https://github.com/r-lib/backports/issues/83 Hi all, I forwarded the issue upstream. I hope they fix it themselves and we can close this bug with a routine upload. Have a nice day, Charles Le Mon, Jul 29, 2024 at 07:56:49AM +0200, Paul Gevers a écrit : > Source: r-c

Bug#1076615: [R-pkg-team] Bug#1076615: r-cran-metamix: autopkgtest regression with rmpi 0.7-2-2 (armel, armhf, i386)

2024-07-21 Thread Charles Plessy
hp?package=rmpi > [2] https://buildd.debian.org/status/package.php?p=rmpi > > -- > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > > ___ > R-pkg-team mailing list > r-pkg-t...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bi

Bug#1074529: [R-pkg-team] Bug#1074529: r-cran-dimred: autopkgtest regression with r-base 4.4.1 (i386)

2024-07-01 Thread Charles Plessy
hecks/check_results_dimRed.html Hello everybody, among the tested release architectures, only i386 is failing. I can update r-cran-dimred so that it excludes i386. But would that mean I have to do that for its reverse-dependencies too ? Have a nice day, Charles -- Charles Plessy

Bug#1073106: marked as pending in swarm-cluster

2024-06-13 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1073106 in swarm-cluster 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/swarm-cluster/-/commit/790cc43073aa1d80e2b

Bug#1073105: marked as pending in ssake

2024-06-13 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1073105 in ssake 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/ssake/-/commit/e182ba7de0f9b15d434fec946810055d09a

Bug#1073104: marked as pending in srst2

2024-06-13 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1073104 in srst2 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/srst2/-/commit/5f8b6e6042855ddba33a608e8541be06330

Bug#1073103: marked as pending in scythe

2024-06-13 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1073103 in scythe 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/scythe/-/commit/953eea5245cbf129820dc601f3c0669fe

Bug#1073098: marked as pending in libvcflib

2024-06-13 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1073098 in libvcflib 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/libvcflib/-/commit/becbc3630213bcc3e3137abdd79

Bug#1073095: marked as pending in hilive

2024-06-13 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1073095 in hilive 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/hilive/-/commit/904fb9ec71de3d067f31607f6d7998a4f

Bug#1073090: marked as pending in alter-sequence-alignment

2024-06-12 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1073090 in alter-sequence-alignment 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/alter-sequence-alignment/-/comm

Bug#1073089: marked as pending in adapterremoval

2024-06-12 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #1073089 in adapterremoval 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/adapterremoval/-/commit/7fa0487843be8a1e3

Bug#1072979: [Debian-med-packaging] Bug#1072979: beast-mcmc - build-dependencies unsatisfiable on i386.

2024-06-11 Thread Charles Plessy
h-specific removals were handled automatically. That would save everybody a lot of work! Cheers, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med Tooting from work,

Bug#1061344: User input needed: Stop supporting 32 bit architectures with emboss (Was: emboss-lib: identified for time_t transition but no ABI in shlibs)

2024-01-30 Thread Charles Plessy
Hi Andreas, I agree that we can remove EMBOSS in all 32-bit platforms. I think that a large fraction of the scientific field has no appetite to do any extra volunteer work to such as accepting our patches to support scientific computations on 32-bit systems in 15 years... Have a nice day, Charl

Bug#1041556: [R-pkg-team] Bug#1041556: What is the architecture name in R what we call armel/armhf

2023-08-17 Thread Charles Plessy
Le Thu, Aug 17, 2023 at 07:52:35AM +0200, Andreas Tille a écrit : > > arch <- R.version$arch > identical(arch, "i386") || identical(arch, "i686") || identical(arch, > "armel") || identical(arch, "armhf") Hi Andreas, how about: system("dpkg-architecture -qDEB_BUILD_ARCH", intern=TRUE) %i

Bug#1042776: [R-pkg-team] Bug#1042776: Bug#1042776: r-bioc-deseq: still depends on obsolete r-api-bioc-3.16

2023-07-31 Thread Charles Plessy
Le Tue, Aug 01, 2023 at 09:29:59AM +0900, Charles Plessy a écrit : > > the DESeq Bioconductor package was removed from the 3.17 release > upstream. I think that we can remove it from unstable and testing too. > > I will fill a removal later today. Actually it was removed from Bi

Bug#1042776: marked as pending in r-bioc-deseq

2023-07-31 Thread Charles Plessy
/bad370412269ea6b7543b3f76d238f1765e3affd r-bioc-deseq (1.39.0-12) unstable; urgency=medium * Team upload. * Update patch to rebuild for BioC API 3.17 (Closes: #1042776) -- Charles Plessy Tue, 01 Aug 2023 11:41:09 +0900

Bug#1042776: [R-pkg-team] Bug#1042776: r-bioc-deseq: still depends on obsolete r-api-bioc-3.16

2023-07-31 Thread Charles Plessy
7 release upstream. I think that we can remove it from unstable and testing too. I will fill a removal later today. Have a nice day, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med Too

Bug#1022307: [Debian-med-packaging] Bug#1022307: status on t_coffee causing biopython ftbfs

2022-11-22 Thread Charles Plessy
lar version may build fine, and let biophython pass its tests, we do not know if t_coffee produces sound results on these architectures. Unless we know or hear from an ARM user, I would recommend to play safe and only distribute it on amd64 for this release. Have a nic

Bug#1023230: [Debian-med-packaging] Bug#1023230: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours

2022-10-31 Thread Charles Plessy
ink that t-coffee never worked on ARM. It built, but never worked. The simplest would be to distribute it only on amd64. See https://bugs.debian.org/631249 Have a nice day, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http

Bug#946850: [Debian-med-packaging] Bug#946850: last-align ftbfs on non-x86 architectures

2019-12-18 Thread Charles Plessy
Le Wed, Dec 18, 2019 at 09:35:44AM +0100, Michael Crusoe a écrit : > > dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow last-align Hi Michael, I ran the commmand a bit more than one hour ago. My Debian skills are a bit rusty; I am not sure if I should receive an automatic email fe

Bug#946850: LAST build fails on non-amd64 platforms.

2019-12-17 Thread Charles Plessy
find portability bugs such as this one). What would you prefer ? Have a nice day, Charles -- Charles Plessy Akano, Uruma, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med Tooting from work, https://mastodon.techn

Bug#890117: Bug #890117 in bedtools marked as pending

2019-02-14 Thread Charles Plessy
. -- Charles Plessy Thu, 14 Feb 2019 22:11:21 +0900 (this message was generated automatically) -- Greetings https://bugs.debian.org/890117

Bug#890117: Bug #890117 in bedtools marked as pending

2019-02-13 Thread Charles Plessy
Control: tag -1 pending Hello, Bug #890117 in bedtools 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/bedtools/commit/25d45b7a051249d4c482fb5095a9bf45

Bug#890117: bedtools FTBFS on big endian: Tools failing: bamtobed bamtofastq coverage genomecov groupby intersect jaccard map merge multicov negativecontrol

2019-02-11 Thread Charles Plessy
Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Akano, Uruma, Okinawa, Japan

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

2017-11-07 Thread Charles Plessy
(to be re-added) symbols file. Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan

Bug#861333: r-base: R packages uploaded to Debian before 14 April 2017 that use .C or .Fortran fail to find objects

2017-04-30 Thread Charles Plessy
what has been done until now. Not supporting partial upgrades puts the maintainers of the r-cran and r-bioc packages between the hammer and the anvil. This said, I think that we have made constant progresses over the years, so I do not feel shy saying "not yet" to the Release team again

Bug#859255: binNMU needed for more R packages.

2017-03-31 Thread Charles Plessy
nomicalignments_1.10.0-1 . ANY . -m "Rebuild for R 3.3.3." Note to debian-science: there are also R CRAN packages that fail with R 3.3.3, (r-cran-lubridate, r-cran-spam), but I am not yet sure if a binNMU is enough. Have a nice day, Charles -- Charles Plessy Debian Med packaging team

Bug#858183: binNMU needed for r-bioc- packages broken by R 3.3.3.

2017-03-19 Thread Charles Plessy
ctors_0.12.1-2 . ANY . -m "Rebuild for R 3.3.3." nmu r-bioc-iranges_2.8.1-1-m . ANY . "Rebuild for R 3.3.3." nmu r-bioc-genomicranges_1.26.2-1 . ANY -m "Rebuild for R 3.3.3." Otherwise I can prepare a more extensive list of packages to rebuild. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan

Bug#857466: marked as done (r-base: CVE-2016-8714: R: Buffer overflow in the LoadEncoding functionality)

2017-03-15 Thread Charles Plessy
Hi Dirk and Salvatore, > From: Dirk Eddelbuettel > On 11 March 2017 at 17:56, Salvatore Bonaccorso wrote: > | > | The relevant changes seem to be the following, but I might be mistaken. > (btw, > | is there a VCS repository for r-base or does upstream not share development > | VCS?) > > They d

Bug#845505: sra-sdk 2.7.0-1 is broken libncbi-vdb2 2.8.0+dfsg-1

2016-11-23 Thread Charles Plessy
Package: sra-sdk Severity: grave Hi all, quick note from work; sorry to not being able to go deeper. A colleague has reported to me that sra-sdk 2.7.0-1 is broken libncbi-vdb2 2.8.0+dfsg-1. For instance: fastq-dump fastq-dump: symbol lookup error: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so.2: un

Bug#831833: [Debian-med-packaging] Bug#831833: Tagged as fixed-upstream - do you intend to upload?

2016-11-03 Thread Charles Plessy
> On Wed, Nov 02, 2016 at 09:03:45PM +0900, Charles Plessy wrote: > > > > I was hoping that Upstream would make a new release with the fix :( > > > > So one would need to check if the following commit would be enough as a > > patch... > > > &

Bug#831833: Tagged as fixed-upstream - do you intend to upload?

2016-11-02 Thread Charles Plessy
Le Wed, Nov 02, 2016 at 12:52:58PM +0100, Andreas Tille a écrit : > > you have set #831833 as fixed-upstream at 20 Jul 2016. Do you intend to > upload the fix to the Debian archive? Hi Andreas, I was hoping that Upstream would make a new release with the fix :( So one would need to check if th

Bug#838748: Bug#695327: Patch pending for cloud-init bugs 838748, 780637 and 695327

2016-09-24 Thread Charles Plessy
Le Sat, Sep 24, 2016 at 03:34:52PM +0200, Nicolas Braud-Santoni a écrit : > Control: tag -1 pending > X-Debbugs-CC: hol...@debian.org > > Hi, > > I prepared an upload for a new version of cloud-init which fixes > (among other things) this bug. It is currently available in the > v0.7.8/master bra

Bug#831833: Processed: Re: [Debian-med-packaging] bedtools is marked for autoremoval from testing

2016-07-26 Thread Charles Plessy
Control: tag -1 +sid Le Wed, Jul 27, 2016 at 05:03:05AM +, Debian Bug Tracking System a écrit : > Processing control commands: > > > notfound -1 2.25.0-1 > Bug #831833 [src:bedtools] bedtools groupby broken; will break users > pipelines. > Ignoring request to alter found versions of bug #831

Bug#831833: [Debian-med-packaging] bedtools is marked for autoremoval from testing

2016-07-26 Thread Charles Plessy
break users pipelines. This bug only affects the new upstream release. -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan

Bug#831833: [Debian-med-packaging] Bug#831833: Command `groupby` broken; will break users pipelines.

2016-07-19 Thread Charles Plessy
Control: retitle -1 bedtools groupby broken; will break users pipelines. Control: forwarded -1 https://github.com/arq5x/bedtools2/issues/418 Control: tag -1 +confirmed Marking as forwarded now that commented in the issue. The command is completely broken, but unfortunately the regression tests fo

Bug#831833: Command `groupby` broken; will break users pipelines.

2016-07-19 Thread Charles Plessy
Source: bedtools Version: 2.26.0-1 Severity: serious Tags: upstream Hi all, at work I was just bitten by upstream issue 418, reporting that `bedtools groupby` is broken. https://github.com/arq5x/bedtools2/issues/418 I am filing this bug to prevent migration to Squeeze. Have a nice day, -- Ch

Bug#823673: samtools: FTBFS in testing

2016-05-08 Thread Charles Plessy
package required a change recently for htslib 1.3.1. > However, if this only builds now with libhts >= 1.3.1, then the > Build-Depends field should be updated accordingly. Thanks for the report; the issue was already reported in #822701, which I just fixed by updating Build-Depends. Have a nice Sunday, -- Charles Plessy Tsurumi, Kanagawa, Japan

Bug#822701: [Debian-med-packaging] Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure;

2016-04-26 Thread Charles Plessy
Control: tag -1 +pending Le Wed, Apr 27, 2016 at 10:12:31AM +0900, Charles Plessy a écrit : > > Perhaps we also need htslib 1.3.1 to "Break" samtools < 1.3.1... I cloned > this bug to address that issue. Hi all, I added: "Breaks: samtools (<< 1.3.1)". I t

Bug#822701: [Debian-med-packaging] Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure;

2016-04-26 Thread Charles Plessy
clone 822701 -2 reassign -2 htslib retitle -2 htslib 1.3.1 breaks samtools 1.3, at least at build time. retitle 822701 samtools 1.3 fails to build against htslib 1.3.1. tag 822701 +pending Le Tue, Apr 26, 2016 at 07:02:28PM +0100, Chris Lamb a écrit : > Source: samtools > Version: 1.3-1 > Severity

Bug#796114: Phasing out libnetty-java (was Re: Bug#796114: CVE-2015-2156)

2015-08-20 Thread Charles Plessy
Le Thu, Aug 20, 2015 at 05:27:34PM +0200, Emmanuel Bourg a écrit : > Le 20/08/2015 13:40, Charles Plessy a écrit : > > > Is that because of incompatibility ? If libnetty-java is still needed, > > would > > it be possible to transfer it under the umbrella of the De

Bug#796114: Phasing out libnetty-java (was Re: Bug#796114: CVE-2015-2156)

2015-08-20 Thread Charles Plessy
that because of incompatibility ? If libnetty-java is still needed, would it be possible to transfer it under the umbrella of the Debian Java team ? Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan

Bug#795847: [Debian-med-packaging] Bug#795847: jellyfish: FTBFS: error: 'struct std::__cxx11::basic_stringbuf<_CharT, _Traits, _Alloc>::__xfer_bufptrs' redeclared with different access

2015-08-19 Thread Charles Plessy
Le Mon, Aug 17, 2015 at 12:46:40PM +0100, Chris Lamb a écrit : > Source: jellyfish > Version: 2.2.3-1 > Severity: serious > Justification: fails to build from source > User: reproducible-bui...@lists.alioth.debian.org > Usertags: ftbfs > X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org >

Bug#792442: [pkg-eucalyptus-maintainers] Bug#792442: jsilver: Should this package be removed?

2015-07-14 Thread Charles Plessy
> > Should we remove it? Thanks Moritz for the heads up. I agree to remove it: I do not see manpower anymore here, and on my side, I would not be able to provide assistance in case a serious bug would be found. Have a nice day, Charles -- Charles Plessy Tsurumi, Kanagawa, Japan sig

Bug#762647: [Debian-med-packaging] Bug#762647: samtools: FTBFS: test suite errors

2015-06-18 Thread Charles Plessy
Le Thu, Jun 18, 2015 at 11:25:46PM -0400, Aaron M. Ucko a écrit : > > I'm glad to see those platforms are doing better now, but that was only > part of the problem. There are still unexpected failures on i386 and > kfreebsd-i386 (though the count's dropped from 95 to 2, a big improvement): > >

Bug#780637: cloud-init: needs to be build in the cloud

2015-03-17 Thread Charles Plessy
Le Tue, Mar 17, 2015 at 10:15:38AM +0100, Holger Levsen a écrit : > > building the cloud-init package fails during package tests because the > hostname metadata.google.internal cannot be resolved and cloud specific URLs > like http://169.254.169.254/openstack/latest cannot be accessed, see attac

Bug#769219: function moved

2014-11-16 Thread Charles Plessy
Le Sun, Nov 16, 2014 at 12:36:05AM +0100, Bill Allombert a écrit : > > Do you know if there is a org to XML (or SGML) conversion option ? Hi Bill, according to its documentation, Pandoc can do convert Org-Mode to DocBoox Have a nice Sunday, -- Charles -- To UNSUBSCRIBE, email to debian-bug

Bug#763218: [Debian-med-packaging] Bug#763218: python-pysam: FTBFS: Tests failures

2014-09-29 Thread Charles Plessy
.py", line 303, in setUp samtools_version )) ValueError: versions of pysam/samtools and samtools differ: 0.1.19 != 1.1 Given that samtools is still at version 0.1.19 in Jessie and that it is unsure whether the version in sid (1.1) will migrate before the Freeze, I am removin

Bug#762647: [Debian-med-packaging] Bug#762647: samtools: FTBFS: test suite errors

2014-09-23 Thread Charles Plessy
issues, but I do not know if the problem is likely to be solved in the short term. https://github.com/samtools/samtools/issues/268 Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRI

Bug#756780: Status bowtie + tophat (Was: [Help] Need help for architecture specific code)

2014-08-24 Thread Charles Plessy
, and given that most users will want to use Bowtie 2 with TopHat, how about solution 2 ? Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org

Bug#755333: [pkg-eucalyptus-maintainers] Bug#755333: wsdl2c: FTBFS: [javac] /«PKGBUILDDIR»/src/org/apache/axis2/builder/MultipartFormDataBuilder.java:28: error: package javax.servlet.http does not exi

2014-07-22 Thread Charles Plessy
Le Tue, Jul 22, 2014 at 01:47:49PM -0300, Miguel Landaeta a écrit : > > This is just about a missing jar file in the classpath of the > compilation. > diff -Nru wsdl2c-0.1/debian/rules wsdl2c-0.1/debian/rules > --- wsdl2c-0.1/debian/rules 2012-06-23 04:07:09.0 -0300 > +++ wsdl2c-0.1/de

Bug#751255: TreeView X abandonned upstream … (was: Re: [Debian-med-packaging] Processed: severity of 751255 is serious).

2014-07-21 Thread Charles Plessy
maintainers of the treeviewx packages there to see if they have found a solution on their side. Thanks again, and have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@list

Bug#755333: [pkg-eucalyptus-maintainers] Bug#755333: wsdl2c: FTBFS: [javac] /«PKGBUILDDIR»/src/org/apache/axis2/builder/MultipartFormDataBuilder.java:28: error: package javax.servlet.http does not

2014-07-21 Thread Charles Plessy
sure what to do. Is that due to some transition ? Shall I just wait and try again in a couple of weeks ? (The VCS URL of the package is svn+ssh://svn.debian.org/svn/svn/pkg-eucalyptus) Have a nice day, -- Charles Plessy, Tsurumi, Kanagawa, Japan Le Sat, Jul 19, 2014 at 08:34:02PM +0200

Bug#753210: [Debian-med-packaging] Bug#753210: bamtools: FTBFS: Patch failed

2014-06-29 Thread Charles Plessy
/dh-exec usr/lib/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH}/ Debhelper does the rest. See https://wiki.debian.org/Multiarch/Implementation for details. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCR

Bug#736565: [Debian-med-packaging] Bug#736565: NMU patch for staden-io-lib 1.13.5-1.1

2014-04-02 Thread Charles Plessy
Le Wed, Apr 02, 2014 at 07:10:23PM +1100, Aníbal Monsalve Salazar a écrit : > > I just submitted Aleksandar Zlicic's patch to upstream. > > https://sourceforge.net/p/staden/bugs/105/ Thanks a lot for this ! -- Charles -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with

Bug#736565: [Debian-med-packaging] Bug#736565: Bug#736565: FTBFS on non-"PC" architectures: FAIL: scram_mt.test

2014-03-31 Thread Charles Plessy
ker on SourceForge: <http://sourceforge.net/p/staden/bugs/>, which is a better place for providing patches. Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-

Bug#736565: [Debian-med-packaging] Bug#736565: FTBFS on non-"PC" architectures: FAIL: scram_mt.test

2014-03-30 Thread Charles Plessy
where it does not build. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org

Bug#741221: Need more (legal) information

2014-03-25 Thread Charles Plessy
rd to the SKIP codes, Mr Halpern draws your attention to the statement he has prepared on the matter, which is included at Appendix F.” To me, it appears that Appendix F, which has non-Free clauses, applies. Have you tried to contact the authors of KANJIDIC ? Have a nice day, -- Charles Pless

Bug#736565: [Debian-med-packaging] Bug#736565: FTBFS on non-"PC" architectures: FAIL: scram_mt.test

2014-03-15 Thread Charles Plessy
Le Sat, Mar 15, 2014 at 01:32:40PM +0900, Charles Plessy a écrit : > Le Mon, Mar 10, 2014 at 12:13:34AM +1100, Aníbal Monsalve Salazar a écrit : > > On Sun, Mar 09, 2014 at 07:58:25PM +0900, Charles Plessy wrote: > > > > > > Speaking of Upstream, I see a new release,

Bug#736565: FTBFS on non-"PC" architectures: FAIL: scram_mt.test

2014-03-14 Thread Charles Plessy
Le Mon, Mar 10, 2014 at 12:13:34AM +1100, Aníbal Monsalve Salazar a écrit : > On Sun, Mar 09, 2014 at 07:58:25PM +0900, Charles Plessy wrote: > > > > Speaking of Upstream, I see a new release, version 1.13.5. Would you > > like me to upload it ? > > Yes, please. Uplo

Bug#741288: [Debian-med-packaging] Bug#741288: seqan: FTBFS on many buildds due to RAM exhaustion

2014-03-10 Thread Charles Plessy
nless you want public researchers to buy more computers with your tax money. Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a s

Bug#736565: FTBFS on non-"PC" architectures: FAIL: scram_mt.test

2014-03-09 Thread Charles Plessy
d to contact the upstream author ? Speaking of Upstream, I see a new release, version 1.13.5. Would you like me to upload it ? Cheers, Charles -- Charles Plessy Debian Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-r

Bug#739575: [Debian-med-packaging] Bug#739575: Bug#739575: python-pysam-tests: world writable directory tree: /var/lib/pysam/tests

2014-02-20 Thread Charles Plessy
Le Thu, Feb 20, 2014 at 10:36:57AM +0100, Andreas Tille a écrit : > > While I agree that this would solve this formal problem I think > providing (potentially large chunks of) data which are only to run a > test and force people to create various copies of them is an insane > consequence of the re

Bug#739575: [Debian-med-packaging] Bug#739575: python-pysam-tests: world writable directory tree: /var/lib/pysam/tests

2014-02-20 Thread Charles Plessy
ite permissions. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org

Bug#736407: [Debian-med-packaging] Bug#736407: staden-io-lib: FTBFS on non-x86 architectures

2014-01-24 Thread Charles Plessy
Control: severity -1 wishlist Le Thu, Jan 23, 2014 at 12:17:40PM +0100, Andreas Beckmann a écrit : > Package: staden-io-lib > Version: 1.13.3-2 > Severity: serious > Justification: fails to build from source > > staden-io-lib only built successfully on i386-any and amd64-any, all > other architec

Bug#732408: pv-grub-menu: fails to install: /usr/sbin/update-menu-lst: line 116: grub: command not found

2014-01-10 Thread Charles Plessy
why. Do you have an explanation ? In the meantime, I am downgrading the severity of this bug: I have confirmed in a minimal system (Debian image for the Amazon cloud) that pv-grub-menu is installable. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debi

Bug#732408: pv-grub-menu: fails to install: /usr/sbin/update-menu-lst: line 116: grub: command not found

2013-12-18 Thread Charles Plessy
the error is there but it does not interrupt the installation. Does piuparts pass some special parameters to the shell to make it more sensible to errors ? Nevertheless, I will fix this bug anyway. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to d

Bug#729276: [Debian-med-packaging] Bug#729276: staden-io-lib-utils: bufferoverflow in index_tar

2013-11-30 Thread Charles Plessy
Le Sat, Nov 30, 2013 at 04:01:50AM -0500, Sang Kil Cha a écrit : > > Yes I think I did submitted it to upstream. Hi again, I do not see it in the Upstream bugtracker. Can you also submit it there ? http://sourceforge.net/p/staden/bugs/ Have a nice Sunday, -- Charles Plessy Debi

Bug#729276: staden-io-lib-utils: bufferoverflow in index_tar

2013-11-30 Thread Charles Plessy
thanks for the report. Have you also submitted it upstream ? Do you have a suggestion on how to solve the problem ? Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.

Bug#729785: Copyright review for the package libpqxx 4.0.1-2.

2013-11-17 Thread Charles Plessy
missing from the Debian copyright file. Have a nice Sunday, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Conta

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