Re: [Bioc-devel] Unexpected Build Failure for BulkSignalR

Hi, On Sat, Apr 12, 2025 at 3:21 PM Jean-Philippe Villemin wrote: > Dear Bioconductor team, > > We were surprised to see that the build of our package BulkSignalR has > recently failed, although it was successful in previous snapshots. We > haven't made any changes to the package since the last

Re: [Bioc-devel] WARNING from Rgl package

can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Moonlight2R) On Fri, Apr 4, 2025 at 3:31 PM Martin Grigorov wrote: > Hi, > > On Fri, 4 Apr 2025 at 14:00, Matteo Tiberti via Bioc-devel < > bioc-devel@r-project.org

Re: [Bioc-devel] WARNING from Rgl package

Hi, On Fri, 4 Apr 2025 at 14:00, Matteo Tiberti via Bioc-devel < bioc-devel@r-project.org> wrote: > Dear all, > > We are seeing the same warning from the builders for our MoonlightR and > Moonlight2R packages, on kungpeng2 only: > > * checking whether package ‘Moonlight2R’ can be installed ... WA

Re: [Bioc-devel] Package Installation Fails on Linux Kunpeng2 Due to ‘concaveman’ and ‘sf’ Dependencies

ine-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘CARDspa_0.99.7.tar.gz’ The next build should be fine! On Thu, Mar 27, 2025 at 9:44 AM Martin Grigorov wrote: > I found a work

Re: [Bioc-devel] Package Installation Fails on Linux Kunpeng2 Due to ‘concaveman’ and ‘sf’ Dependencies

/share/proj The 'sf' build is still running! On Thu, Mar 27, 2025 at 9:27 AM Martin Grigorov wrote: > Using libgdal-core 3.x fails with: > > > BiocManager::install(c("sf")) > Bioconductor version 3.21 (BiocManager 1.30.25), R Under development > (unstable

Re: [Bioc-devel] Package Installation Fails on Linux Kunpeng2 Due to ‘concaveman’ and ‘sf’ Dependencies

nfiguration failed for package ‘sf’ * removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/sf’ gdal 2.x does not provide linux-aarch64 builds, so i cannot try it :-/ Any ideas are welcome ! On Thu, Mar 27, 2025 at 8:52 AM Martin Grigorov wrote: > Hi, > > The problem is a trans

Re: [Bioc-devel] Package Installation Fails on Linux Kunpeng2 Due to ‘concaveman’ and ‘sf’ Dependencies

Hi, The problem is a transitive dependency: * installing *source* package ‘sf’ ... ** this is package ‘sf’ version ‘1.0-20’ ** package ‘sf’ successfully unpacked and MD5 sums checked ** using staged installation configure: CC: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -s

Re: [Bioc-devel] New version of rmspc - error

Hi, I've installed .NET 9 at kunpeng2 and taishan machines. The next builds should be fine/better ! Regards, Martin On Mon, Mar 17, 2025 at 4:45 AM Meriem Bahda wrote: > Hi Lori, > > I see that the error in all servers is *System command 'dotnet' failed, > *which > means this is an issue relat

Re: [Bioc-devel] C++ compiler error on kunpeng2 ?

Hi, Installed the tbb-devel package! The next build should be fine! Thanks for the report! Regards, Martin On Mon, Mar 10, 2025 at 1:39 PM Martin Grigorov wrote: > Hi, > > I’ll check which package needs to be installed to provide libtbbmalloc! > > On Mon, 10 Mar 2025

Re: [Bioc-devel] C++ compiler error on kunpeng2 ?

Hi, I’ll check which package needs to be installed to provide libtbbmalloc! On Mon, 10 Mar 2025 at 13:19, Katja Danielzik < katja.daniel...@stud.uni-due.de> wrote: > Dear all, > > i have noticed that my package "MetaboDynamics" which employs stan > models ,that are pre-compiled to C++ during ins

Re: [Bioc-devel] Package check errors Fwd: seqArchR problems reported in the Multiple platform build/check report for BioC 3.21

dates. I've updated the symlinks to use /usr/bin/python3.11 ! Let's see what the next build will show! On Fri, Dec 27, 2024 at 11:35 AM Martin Grigorov wrote: > Hi, > > I have installed scikit-learn at Tuesday: > > biocbuild@kunpeng2 ~/git [1]> python -m pip install s

Re: [Bioc-devel] Package check errors Fwd: seqArchR problems reported in the Multiple platform build/check report for BioC 3.21

nductor Core Team > -- > *From:* Bioc-devel on behalf of Martin > Grigorov > *Sent:* Monday, December 9, 2024 3:34 AM > *To:* Sarvesh Nikumbh > *Cc:* Bioc-devel > *Subject:* Re: [Bioc-devel] Package check errors Fwd: seqArchR problems > re

Re: [Bioc-devel] Package check errors Fwd: seqArchR problems reported in the Multiple platform build/check report for BioC 3.21

Hi, This issue should be fixed on kunpeng2 in the next build run (the results will be available two days from now). Regards, Martin On Tue, Dec 3, 2024 at 7:58 PM Sarvesh Nikumbh wrote: > Dear Bioc team, > > I am seeing check errors on nebbiolo1 and palomino7 and build and install > error on k

Re: [Bioc-devel] DeepTarget error built in Linux (openEuler 22.03 LTS-SP1) / aarch64

Hi, This has been fixed earlier today. It should be OK in the next run (tomorrow). Regards, Martin On Fri, 25 Oct 2024 at 17:47, Nguyen, Trinh (NIH/NCI) [C] via Bioc-devel < bioc-devel@r-project.org> wrote: > > Dear Developers, > > Could you please guide me what I should do? I received an error

Re: [Bioc-devel] WARNING on builders from rgl package

Hi Matteo, I see your package failed on kunpeng2 (Linux ARM64) - https://bioconductor.org/checkResults/3.20/bioc-LATEST/MoonlightR/kunpeng2-buildsrc.html This issue has been fixed earlier today. It was reported by Oleksii here on the mailing list. It should be OK in the next build (tomorrow). Sorr

Re: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

gmail.com> wrote: > >> Thanks very much! >> >> Oleksii >> >> On Wed, 23 Oct 2024 at 10:52, Martin Grigorov >> wrote: >> >>> Hi Oleksii, >>> >>> On Wed, Oct 23, 2024 at 9:47 AM Oleksii Nikolaienko < >>> oleksii.

Re: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

conda for installing newer versions of dependencies than the ones in the OS repos. Martin > Best, > Oleksii > > On Wed, 23 Oct 2024 at 08:33, Martin Grigorov > wrote: > >> Hi, >> >> The problem was missing rustc and cargo on kunpeng2: >> ==

Re: [Bioc-devel] Kunpeng2 compilation error -lopenblas

Hi, This issue has been fixed earlier today. It should be OK in the next build (tomorrow). Regards, Martin On Wed, Oct 23, 2024 at 11:28 AM Morgan, Michael via Bioc-devel < bioc-devel@r-project.org> wrote: > Hi Bioc team, > I’m the maintainer of miloR. I have a build compilation error on kunpen

Re: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

Hi, The problem was missing rustc and cargo on kunpeng2: = /bin/sh: line 2: rustc: command not found Rust version: /bin/sh: line 3: cargo: command not found Cargo version: /bin/sh: line 11: cargo: command not found make: *** [Makevars:25: /home/b

Re: [Bioc-devel] Mac arrow installation problem causing R CMD check fail

Hi, On Thu, 22 Aug 2024 at 18:12, Dongyi Lu wrote: > Hi, > > My packages have been failing R CMD check on the Bioc server on Mac because > of this error: > > unable to load shared object > > '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so': > > > dlopen

Re: [Bioc-devel] Build error for cfTools

Hi Ran, Do you remember how it was solved before (for kunpeng2) ? https://anaconda.org/conda-forge/tensorflow does not provide linux-aarch64 build even for 2.17.0 in the conda-forge channel. Your package uses 2.10.0. The anaconda channel does provide it - https://anaconda.org/anaconda/tensorflow,

Re: [Bioc-devel] Devel build report errors

On Mon, Jul 8, 2024 at 11:21 AM Martin Grigorov wrote: > Hi, > > > On Mon, 8 Jul 2024 at 11:14, Rodrigo Arcoverde Cerveira < > rodrigo.arcove...@gmail.com> wrote: > >> Hi all, >> >> We are trying to implement a new tool in scifer package, and I have

Re: [Bioc-devel] Devel build report errors

Hi, On Mon, 8 Jul 2024 at 11:14, Rodrigo Arcoverde Cerveira < rodrigo.arcove...@gmail.com> wrote: > Hi all, > > We are trying to implement a new tool in scifer package, and I have a few > questions about compatibility and build reports. > > 1. I am getting the following error in build for Lin

Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

Hi, Yesterday there was another email about Biostrings - https://stat.ethz.ch/pipermail/bioc-devel/2024-April/020395.html I thought it might be related to your problem. Regards, Martin On Thu, Apr 25, 2024 at 8:23 AM Ulrich Bodenhofer < ulrich.bodenho...@gmail.com> wrote: > Dear colleagues, dea

Re: [Bioc-devel] Incorrect warning about failing package built

_version: 1.26.3 ReactomeGSA.data is installed on kunpeng2! Regards, Martin On Mon, Feb 5, 2024 at 12:08 PM Martin Grigorov wrote: > Hi again, > > I tried to find the problem by (un)installing any (pip) global > installations of pandas, leidenalg, umap-learn, igraph and python-igraph, &

Re: [Bioc-devel] Check time on macOS (MIRit)

Hi Kasper, According to https://github.com/Bioconductor/BBS/blob/9ebb2cf20e70e4bebf24a2a824a67193de821b08/3.19/bioc-mac-arm64/kjohnson3/config.sh#L17-L20 the machine has 24 vCPUs. The automatic/weekly build utilizes 12-16 out of those at any given time! With the respective RAM and disk usage. By

Re: [Bioc-devel] Incorrect warning about failing package built

FICATION=C time zone: UTC tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] reticulate_1.35.0 loaded via a namespace (and not attached): [1] compiler_4.4.0 Matrix_1.6-5 cli_3.6.2 tools_4.4.0

Re: [Bioc-devel] Incorrect warning about failing package built

Hi, Here is the issue - https://github.com/TomKellyGenetics/leiden/issues/26 I realized that we have discussed it a few months back! Martin On Sun, Feb 4, 2024 at 10:27 PM Martin Grigorov wrote: > Hi , > > ReactomeGSA.data package fails to install because it depends on leiden and

Re: [Bioc-devel] Incorrect warning about failing package built

s "feature" can help a vignette succeed even if it's broken. For example > if ReactomeGSA got loaded by a previous vignette then evaluation of > reanalysing-public-data.Rmd would still succeed even though it doesn't do > 'library(ReactomeGSA)'. > > To co

Re: [Bioc-devel] Incorrect warning about failing package built

Hi, On Thu, 1 Feb 2024 at 23:05, Jennifer Wokaty wrote: > Hi Johannes, > > Looking at R CMD Check on devel, it looks like you're missing a > `library(ReactomeGSA)` in reanalysing-public-data.Rmd, which is why it > doesn't find the function `get_public_species()`. We only build the > vignettes on

Re: [Bioc-devel] build reports for apple silicon

Hi, https://bioconductor.org/checkResults/3.19/bioc-mac-arm64-LATEST/ Regards, Martin On Wed, Jan 24, 2024 at 5:55 PM Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > We're clearly producing binary builds for Apple Silicon. Why do we not have > a build report for this platform? > >

Re: [Bioc-devel] Workflow package build all OK but no vignette and red Package propagation status LED

Hi, If you hover over the red LED you will see the following hint: NO, package depends on 'miRBaseConverter' which is not available" Regards, Martin On Mon, Nov 13, 2023 at 11:31 AM James Perkins wrote: > Hi, > > I am the maintainer of the Workflow package ExpHunterSuite. > > In the build repo

Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

Hi, > quickBamFlagSummary(eh[["EH8081"]]) see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache [E::hts_hopen] Failed to open file /home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133 [E::hts_open_format] Failed to open file "/home/biocbuild/.cac

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

wrote: > Hi Martin, > > Yes, I removed that specified test case that failed the check in order to > meet Bioconductor 3.18 release deadline. > > Thanks again for looking into this! > > Best, > > Reina C. > > On Oct 19, 2023, at 4:20 AM, Martin Grigorov > wrot

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

P_6'=0.40, >'TP_9'=0.38, >'TP_9'=0.52, >'TP_2'=0.44, >'TP_2'=0.40, >'TP_4'=0.44, >

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

On Wed, Oct 18, 2023 at 11:11 PM Chau, Reina wrote: > Thank you both! I will look thru the links and see if I can implement a > fix. > I'd be happy to test any patches if it will be easier for you ! Martin > > Best, > > Reina C. > > On Oct 18, 2023, at 4

Re: [Bioc-devel] groHMM package error

Hi, On Wed, Oct 18, 2023 at 11:31 PM Tulip Nandu wrote: > Hi, > > I just got an email from the Bioconductor stating, > > According to the Multiple platform build/check report for BioC 3.18, > the groHMM package has the following problem(s): > > o ERROR for 'R CMD build' on nebbiolo2. See the de

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

Hi, On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès wrote: > Hi Reina, > > Note that CaDrA results on Mac ARM64 are also affected: > https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/ > > See Martin Grigorov's blog post here > https://blog.bioconductor.org/posts/2023-06-09-deb

Re: [Bioc-devel] Release Package Update Issue

Hi, 3.17 (release) has been frozen: https://stat.ethz.ch/pipermail/bioc-devel/2023-October/019920.html https://stat.ethz.ch/pipermail/bioc-devel/2023-October/019928.html Regards, Martin On Tue, Oct 17, 2023 at 6:59 AM Guy Hunt wrote: > Hi > > I have updated the devel version of my Bioconductor

Re: [Bioc-devel] cfTools build error

Hi, https://pypi.org/project/tensorflow/2.10.0/#files is the first release that provides a wheel for Linux ARM64 (aarch64). Would it be OK to update from 2.8.0 to 2.10.0 ? Or even better to 2.14.0 (latest and greatest)! Regards, Martin On Tue, Oct 10, 2023 at 9:30 PM RAN HU wrote: > Dear Bioc

Re: [Bioc-devel] extraChIPs build error on kunpeng2

Hi, On Tue, Oct 10, 2023 at 10:30 AM Stevie Pederson < stephen.pederson...@gmail.com> wrote: > Hi, > > I've got a build error on kunpeng2 which has me a bit stuck, with the build > report available here: > > https://bioconductor.org/checkResults/3.18/bioc-LATEST/extraChIPs/kunpeng2-checksrc.html

Re: [Bioc-devel] magpie package failing unit test

Dear Daoyu, I can reproduce the test failure at kunpeng2 build runner! I'd be happy to test any suggestions you might have! Regards, Martin On Fri, Sep 22, 2023 at 6:34 PM Daoyu Duan wrote: > Dear Bioconductor team, > > I have received emails that my package "magpie" is failing the unit test >

Re: [Bioc-devel] Including large files for the package

Hello, Perhaps you could use https://bioconductor.r-universe.dev/BiocFileCache to download the big file on demand. The benefit is that the file would be stored in ~/.cache/R/yourPackage/ (for Linux; something similar for Windows/Mac) and reused between sessions. Regards, Martin On Tue, Aug 29, 2

Re: [Bioc-devel] Cherry picking error - SiPSiC package

Any idea? > > > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > Virus-free.www.avast.com > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm

Re: [Bioc-devel] Cherry picking error - SiPSiC package

Hi Daniel, You could try `git cherry-pick -x SHA` instead. Where "SHA" is the commit hash in devel branch. This way you will cherry-pick only your particular commit. - git reset --hard - git switch devel - git log --oneline -1 # to get the SHA - git switch RELEASE_3_17 - git pull --rebase - git

Re: [Bioc-devel] [+externe Mail+] Re: pwOmics package get error message for Linux check

Genomics (NIG), Core Unit > Department of Human Genetics > University Medical Center Göttingen (UMG) > Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany > Contact : 0551 39-60778 > -- > *Von:* Martin Grigorov > *Gesendet:* Dienstag, 8. August 2023 1

Re: [Bioc-devel] Omada package failing due to removed dependency

epherd - Kern >>> >>> Bioconductor Core Team >>> >>> Roswell Park Comprehensive Cancer Center >>> >>> Department of Biostatistics & Bioinformatics >>> >>> Elm & Carlton Streets >>> >>> Buffalo, New York

Re: [Bioc-devel] pwOmics package get error message for Linux check

Hi, On Tue, 8 Aug 2023 at 12:32, Sitte, Maren wrote: > Dear Bioconductor Developers, > > > I received an email that my package "pwOmics" gets an error in the check > under Linux. > Install and build gets an OK, but check shows an error. > > I had a look and the problem seems to be: > > > Bio

Re: [Bioc-devel] Omada package failing due to removed dependency

Hi Sokratis, You need to do "git pull --rebase" before trying to push. Most probably the version has been bumped upstream. Regards, Martin On Mon, Jul 31, 2023 at 2:16 PM Sokratis Kariotis < sokratiskario...@gmail.com> wrote: > Hey all, > > I created a new key and now I can commit etc but there

Re: [Bioc-devel] benchdamic TIMEOUT in merida1 and kunpeng2

HI, I don't have a good explanation why it was timing out on kunpeng2 but I think it will pass from now on! Here is what I did: 1) I tried to build benchdamic on kunpeng2: $ R CMD build --keep-empty-dirs --no-resave-data benchdamic * checking for file ‘benchdamic/DESCRIPTION’ ... OK * preparing

Re: [Bioc-devel] SVMDO Bioc 3.18 Kunpeng2 error

Hi, Last week we updated R from 4.3.0 to 4.3.1 with empty site-library/ folder. All packages are being re-installed and some of them timed out. I just checked and both klaR and org.Hs.eg.db are installed. Please re-check the results later today! Regards, Martin On Tue, Jun 27, 2023 at 11:25 AM

Re: [Bioc-devel] Rhtslib on arm64

Hi Ulrich, The issue with the LOCK files and folders have been addressed with https://github.com/Bioconductor/BBS/pull/291 https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/Rhtslib/kjohnson2-install.html says "This page was generated on 2023-06-02 11:02:20". I guess the issue will b

Re: [Bioc-devel] Cannot push to BioC git repo

Hi Ulrich, Your problem looks like another problem of which the Bioc core team is aware but yours looks a bit different so it might be something new. Last Friday another developer shared this in the Slack #bioc_git channel:

Re: [Bioc-devel] Support for Linux ARM64

ly. > > That could take some time to figure out. > > I conclude that the mechanics of working with ARM64 and R to process > Bioconductor > packages are very tractable, but the work needed to get the whole > ecosystem to a > favorable state, as usable as it is for intel linux

Re: [Bioc-devel] Support for Linux ARM64

em, as long as: > > - R is supported on your ARM64-based Linux machine > > - you have compilers that are supported by R > > - you have the external libraries that are required by some CRAN and/or > Bioconductor packages. > > Hope this helps, > > H. > > On 05

[Bioc-devel] Support for Linux ARM64

Dear community, Happy and successful new year! Appologies if this has been discussed before but https://stat.ethz.ch/pipermail/bioc-devel/ does not provide search facilities and my googling didn't help much! I'd like to ask whether Linux ARM64 is officially supported ? I know that Mac ARM64 is s