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,

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

ion: 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, > a

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

e 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 Rcpp_1.0.12 [

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

SA 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 complicate things even more, it could be that the order in which > vignettes are evaluated is platform-dependent. This

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

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

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

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

'TP_9'=0.38, >'TP_9'=0.52, >'TP_2'=0.44, >'TP_2'=0.40, >'TP_4'=0.44, >'TP_9'=0.49)) > > testthat::expect_equal(round(result$obs_best_sco

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 4:03 P

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

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 >

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

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,

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

gt; > > <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> > Virus-free.www.avast.com > <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> > <#m_1308354042402282384_DAB4FAD8-2DD7

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 -

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

ics (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 14:36:

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

d - Kern >>> >>> Bioconductor Core Team >>> >>> Roswell Park Comprehensive Cancer Center >>> >>> Department of Biostatistics & Bioinformatics >>> >>> Elm & Carlton Streets >>> >>> Buffalo, New York 14263

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: > > >

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

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 *

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

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

rking 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 or mac or windows, may > be laborious. > > OK so maybe a good start would be to try to set

Re: [Bioc-devel] Support for Linux ARM64

4-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 05/01/2023 02:01, Martin Grigorov wrote: > > Dear c

[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