Tag: arm64

[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-azure-5.15/5.15.0.1056.64~20.04.45)

All autopkgtests for the newly accepted linux-meta-azure-5.15 (5.15.0.1056.64~20.04.45) for focal have finished running. The following regressions have been reported in tests triggered by the package: systemd/245.4-4ubuntu3.23 (arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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Unable to install bioconda and bowtie

Unable to install bioconda and bowtie 0 ➜ ~ conda install -c “bioconda/label/cf201901” bowtie Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages…

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autopkgtest regression on architectures where char is unsigned

Source: rust-rusqlite Version: 0.29.0-2 Severity: serious tracker.debian.org/pkg/rust-rusqlite Issues preventing migration: ∙ ∙ autopkgtest for rust-rusqlite/0.29.0-2: amd64: Pass, arm64: Regression or new test ♻ (reference ♻), armel: Regression or new test ♻ (reference ♻), armhf: Regression or new test ♻ (reference ♻), i386: Pass, ppc64el: Reference test in progress, but real…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-nvidia-tegra/5.15.0.1020.20)

All autopkgtests for the newly accepted linux-meta-nvidia-tegra (5.15.0.1020.20) for jammy have finished running. The following regressions have been reported in tests triggered by the package: linux-nvidia-tegra/5.15.0-1020.20 (arm64) wireguard/unknown (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…

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Bug#1058580: flint: autopkgtest regression

Source: flint Version: 3.0.1-1 Severity: serious tracker.debian.org/pkg/flint Migration status for flint (2.9.0-5 to 3.0.1-1): BLOCKED: Rejected/violates migration policy/introduces a regression Issues preventing migration: ∙ ∙ autopkgtest for flint/3.0.1-1: amd64: Regression or new test ♻ (reference ♻), arm64: Regression or new test ♻ (reference ♻), armel: Regression or new test ♻…

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Bug#1056885: sagemath: ftbfs with cython 3.0.x

Control: tags -1 patch On Sun, 26 Nov 2023 10:06:52 +0000 Matthias Klose wrote: If the package cannot be built with cython 3.0.5, please change the build dependency from cython3 to cython3-legacy (available now in unstable). There is no replacement for cython3-dbg. The attached patch switches to cython3-legacy as the…

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Pytorch installation error – General Topics and Other SDKs

Hi ,i have upgrade my cuda from 11,4 to 12.2 using the following steps:wget developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/arm64/cuda-keyring_1.1-1_all.debsudo dpkg -i cuda-keyring_1.1-1_all.debsudo apt-get updatesudo apt-get -y install cudasudo gedit ~/.bashrcexport PATH=/usr/local/cuda-12.2/bin${PATH:+:${PATH}}export LD_LIBRARY_PATH=/usr/local/cuda-12.2/${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}source ~/.bashrc after that i am ablr=e to clone the pytorch using the following steps: git clone –recursive –branch v2.1.1 github.com/pytorch/pytorch export USE_NCCL=0…

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Interaction terms in DESeq2

Hi, I am hoping this isn’t a stupid question as I am really lost here. I have extensively read the manual and other forum posts but am struggling to find a solution. I am using DESeq2 to analyse my data set but running into problems with an interaction term in…

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Bioconductor – IFAA (development version)

DOI: 10.18129/B9.bioc.IFAA   This is the development version of IFAA; for the stable release version, see IFAA. Robust Inference for Absolute Abundance in Microbiome Analysis Bioconductor version: Development (3.19) This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome…

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Panic: Could not run ‘torchvision::roi_pool’ with arguments from the ‘CUDA’ backend – Jetson Nano

Hi, Team! I have such errors, when I run my code in docker container: root@de87551d73cf:/app/src# ./main WARN[0032] CUDA is valid WARN[0044] CUDA is valid INFO[0044] Forwarding… [W TensorImpl.h:1156] Warning: Named tensors and all their associated APIs are an experimental feature and subject to change. Please do not use them for…

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Can’t install hisat2 with miniconda

Can’t install hisat2 with miniconda 0 I’ve been trying to install hisat2 with Miniconda but I keep getting this error. Miniconda is updated and seemingly installed. Also I’m on Mac OS. Please Advise. Channels: bioconda default defaults conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): done Solving environment: failed PackagesNotFoundError: The…

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systemd autopkgtest regression on arm64 and s390x on mantic

Is seems the container fails to boot. From a bad run: 9109s autopkgtest [10:39:17]: test tests-in-lxd: [———————– 9145s 2023-11-28T10:39:50Z INFO Waiting for automatic snapd restart… 9259s lxd 5.19-8635f82 from Canonical** installed 9288s Creating autopkgtest-prepare-jhI 9475s Retrieving image: metadata: 100% (323.81MB/s) Retrieving image: rootfs: 1% (3.53MB/s) <SNIP> Retrieving image: rootfs: 100%…

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[Kernel-packages] [Bug 2039144] Autopkgtest regression report (linux-meta-laptop/6.5.0.1007.10)

All autopkgtests for the newly accepted linux-meta-laptop (6.5.0.1007.10) for mantic have finished running. The following regressions have been reported in tests triggered by the package: systemd/253.5-1ubuntu6.1 (arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-raspi/6.5.0.1008.9)

All autopkgtests for the newly accepted linux-meta-raspi (6.5.0.1008.9) for mantic have finished running. The following regressions have been reported in tests triggered by the package: acpi-call/unknown (arm64) adv-17v35x/unknown (arm64) backport-iwlwifi-dkms/unknown (arm64) bbswitch/unknown (arm64) dahdi-linux/unknown (arm64) ddcci-driver-linux/unknown (arm64) digimend-dkms/unknown (arm64) dm-writeboost/unknown (arm64) dpdk-kmods/unknown (arm64) evdi/unknown (arm64) falcosecurity-libs/unknown (arm64) fwts/unknown (arm64) glibc/unknown…

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Unable to launch RStudio on Ubuntu 22.04 – General

Hi, Sorry for the simple question, but I have had some issues getting RStudio to launch on Ubuntu. I am using Ubuntu 22.04.3. I have R installed, and it is running fine. I installed RStudio as below: sudo apt install -f /home/parallels/rstudio-2023.12.0-daily-323-arm64.deb It seems to run fine, but no icon…

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merge .pdata and .xdata sections from host object files

diff –git a/src/cmd/cgo/internal/test/callback_windows.go b/src/cmd/cgo/internal/test/callback_windows.gonew file mode 100644index 0000000..95e97c9— /dev/null+++ b/src/cmd/cgo/internal/test/callback_windows.go@@ -0,0 +1,133 @@+// Copyright 2023 The Go Authors. All rights reserved.+// Use of this source code is governed by a BSD-style+// license that can be found in the LICENSE file.++package cgotest++/*+#include <windows.h>+USHORT backtrace(ULONG FramesToCapture, PVOID *BackTrace) {+#ifdef _AMD64_+ CONTEXT context;+…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-raspi/5.4.0.1099.129)

All autopkgtests for the newly accepted linux-meta-raspi (5.4.0.1099.129) for focal have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-390/390.157-0ubuntu0.20.04.1 (armhf) openafs/unknown (arm64) openrazer/unknown (arm64) systemd/unknown (arm64) west-chamber/unknown (arm64) wireguard/unknown (arm64) wireguard-linux-compat/unknown (arm64) xtables-addons/unknown (arm64) zfs-linux/unknown (arm64) Please visit the excuses page listed below…

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macos – M2pro Mac opencv c++ failed,but it worked normally serveral days ago

the error are as follows: g++ main.cpp -std=c++14 `pkg-config –cflags –libs opencv4` ./a.out dyld[73360]: Library not loaded: /opt/homebrew/opt/mbedtls/lib/libmbedcrypto.14.dylib Referenced from: <8C2E2CF9-054E-300F-BDE7-3DE52F848638> /opt/homebrew/Cellar/librist/0.2.7_3/lib/librist.4.dylib Reason: tried: ‘/opt/homebrew/opt/mbedtls/lib/libmbedcrypto.14.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/mbedtls/lib/libmbedcrypto.14.dylib’ (no such file), ‘/opt/homebrew/opt/mbedtls/lib/libmbedcrypto.14.dylib’ (no such file), ‘/usr/local/lib/libmbedcrypto.14.dylib’ (mach-o file, but is an incompatible architecture (have ‘x86_64’, need ‘arm64’)), ‘/usr/lib/libmbedcrypto.14.dylib’ (no…

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autopkgtest regression on arm64 and s390x

Source: python-sparse Version: 0.14.0-1 Severity: serious User: debi…@lists.debian.org Usertags: regression Hi Maintainer The upload of python-sparse 0.14.0-1 is failing its own autopkgtest on arm64 and s390x [1][2]. I’ve copied what I hope is the relevant part of the log below. Regards Graham [1] ci.debian.net/packages/p/python-sparse/testing/arm64/ [2] ci.debian.net/packages/p/python-sparse/testing/s390x/ 60s autopkgtest [15:18:15]: test command1: set -e ;…

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132arm64-default][science/votca] Failed for votca-2022.1_1 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere3/data/132arm64-default/d5268d5f7157/logs/votca-2022.1_1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=132arm64-default&build=d5268d5f7157 Log: =>> Building science/votca build started at Fri Nov 10…

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ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications | BMC Bioinformatics

Pipeline architecture and configuration file Genomic data processing poses a challenge for genetic research studies because it involves multiple program dependency installations, vast numbers of samples with raw data from various next-generation sequencing (NGS) platforms, and inconsistent genetic variant ID and/or positions among datasets. The Iliad suite of genomic data…

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SparseArray unable to install on Bioc 3.18

SparseArray unable to install on Bioc 3.18 0 @f33be25c Last seen 6 hours ago United States I have been using DESeq2 now for several months and my code has been working just fine for my analysis. However today I was unable to load the DESeq package. It appears the issue…

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systemtap: autopkgtest regression: Pass 4: compilation failed. [man error::pass4]

Source: systemtap Version: 4.9-1 Severity: serious User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails since a couple of months. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. The release team…

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‘NoneType’ object has no attribute ‘utcoffset’

Source: undertime Version: 3.2.0 Severity: serious Tags: sid trixie User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. The release team has announced…

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Bug#1055392: wasmedge: autopkgtest regression: ‘cstdint’ file not found

Source: wasmedge Version: 0.13.4+dfsg-1 Severity: serious User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. The release team has announced [1] that failing…

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picrust2 installation error on mac m2

I am trying to install Picrust2 on a mac m2 and am getting installation errors regarding incompatible packages (perhaps a type or missing channel).  Looking for: [‘picrust2=2.5.2’] bioconda/osx-arm64                                 124.0 B @ 154.0 B/s  0.8s…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta/6.5.0.12.14)

All autopkgtests for the newly accepted linux-meta (6.5.0.12.14) for mantic have finished running. The following regressions have been reported in tests triggered by the package: network-manager/1.44.2-1ubuntu1.2 (arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘

Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…

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How to apply c++ code after successful pytorch android build? – torch.compile

pytorch build for android was completed as follows. $ ANDROID_NDK=…/android-ndk-r21e $ ANDROID_ABI=”arm64-v8a” $ cd scripts $ ./build_android.sh … (long time) … [100%] Linking CXX static library ../lib/libtorch.a [100%] Built target torch Install the project… — Install configuration: “Release” Installation completed, now you can copy the headers/libs from /mnt/HDD_2TB/greenfish/pytorch_build/work.trial9/pytorch/build_android/install to your…

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r – Issues with rqa in nonlinearTseries version 0.2.12 in RStudio

I am trying to run a simple rqa using nonlinearTseries in R using version 0.2.12 of the library a <- c(1,2,1,2,1,2) a.rqa <- rqa(time.series = a, embedding.dim = 1, time.lag = 1, radius = .1) While I never had any issue with this in the past, I noticed that since…

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Bioconductor – Bioconductor 3.18 Released

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

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Bioconductor – lemur

DOI: 10.18129/B9.bioc.lemur   Latent Embedding Multivariate Regression Bioconductor version: Release (3.18) Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold…

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Custom Z2JH image creation using jupyter-repo2docker – Zero to JupyterHub on Kubernetes

Hello, members. 1. Goal I would like to create a custom image for Z2JH using jupyter-repo2docker command. jupyter-repo2docker github.com/norvig/pytudes works fine. 2. Question Does Z2JH use jupyter-repo2docker for creating a support images (ex. jupyter/pyspark-notebook) ? Is Z2JH base_image jupyter/base-notebook? Does anyone know how to avoid this error? (Maybe macOS docker…

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RStudio Opens from DMG but Not from Applications Folder on Mac – RStudio IDE

Issue: I’ve installed RStudio (Version 2023.09.1+494) on my Mac. However, I got Error Starting R by clicking on the RStudio icon in the Applications folder. Strangely, if I use the DMG file, it opens without any issues, but this is not a convenient way to use the software. System information:…

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r – unable to install Tidyverse in RStudio / Chromebook

I have been trying to install tidyverse via RStudio (R 4.3.1) on my Acer chromebook, but keep having error messages. I have been working my way through these messages with the help of previously asked questions on stackoverflow as well as google and chatGPT I have tried various things and…

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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files

Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…

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Bioconductor – easylift (development version)

DOI: 10.18129/B9.bioc.easylift   This is the development version of easylift; to use it, please install the devel version of Bioconductor. An R package to perform genomic liftover Bioconductor version: Development (3.18) The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with…

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Bug#1040057: #1040057: slixmpp: autopkgtest regression on arm64: Segmentation fault

Hi Martin, On 02-10-2023 08:42, Martin wrote: Finally, I had some time to run the autopkgtest suite on my own arm64 machine (MNT reform). It did not segfault, so I assume a specific problem with the C/I system. I have no idea how to debug this, help is appreciated! If…

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Bugs : pytorch-cuda package : Ubuntu

Mantic package 2.0.1+dfsg-4 FTBFS. At a minimum, this diff in debian/control.cuda is needed: diff –git a/debian/control.cuda b/debian/control.cudaindex 0d0b6c61..4a8f9def 100644— a/debian/control.cuda+++ b/debian/control.cuda@@ -27,7 +27,7 @@ Build-Depends: cmake,                libflatbuffers-dev (<< 2.0.9~),                flatbuffers-compiler-dev,                libfxdiv-dev (>= 0.0~git20200417.b408327~),– libgloo-cuda-dev (>= 0.0~git20230117.1090929~) [amd64 arm64 ppc64el],+ libgloo-dev (>= 0.0~git20230117.1090929~) [amd64 arm64 ppc64el],                libideep-dev (>= 0.0~git20230213.7bc3e12~) [amd64 arm64 ppc64el],                liblapack-dev,                libleveldb-dev,@@ -43,7 +43,7 @@…

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Libtorch make linker error on M2 Mac – C++

sjoptra (S) October 8, 2023, 5:12am 1 Following the exact steps in Installing C++ Distributions of PyTorch — PyTorch main documentation, I created the following file structure as indicatedexample-app/CMakeLists.txtexample-app.cpp when I runmkdir buildcd buildcmake -DCMAKE_PREFIX_PATH=/absolute/path/to/libtorch …cmake –build . –config Release I get the following linker error [ 50%] Building CXX…

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How do you set limits and breaks in a ggplot with an sf object? – tidyverse

By the time it get’s past geom_sf, it’s just an ordinary ggproto object and you can apply the breaks and limits arguments in the ordinary way, such as below (not that one would actually want to for the example) library(ggplot2) library(sf) #> Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0;…

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Bug#1053302: pytorch-sparse: FTBFS on arm64

Source: pytorch-sparse Version: 0.6.17-1 Severity: serious Tags: ftbfs sid trixie Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: sram…@debian.org buildd.debian.org/status/fetch.php?pkg=pytorch-sparse&arch=arm64&ver=0.6.17-1&stamp=1694243524&raw=0 =================================== FAILURES =================================== ________________________ test_spmm[dtype5-device5-sum] _________________________ dtype = torch.float32, device = device(type=’cpu’), reduce = ‘sum’ @pytest.mark.parametrize(‘dtype,device,reduce’, product(grad_dtypes, devices, reductions)) def test_spmm(dtype, device, reduce): if device == torch.device(‘cuda:0’) and dtype…

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rstudio – Creating an R package using roxygen2. Issue with install.packages() , error in use_namespace()?

I have built a local package to handle some data manipulations that I commonly use. My file structure is: -RExample/ — adhoc.R — DESCRIPTION — man/ — function1.Rd — function2.Rd — NAMESPACE — R/ — src_code_1.R RExammple.Rproj Using oxygen2, I build the package: package_dir = “/direct/path/here/R/RExample/” build(package_dir, path=package_dir) The package…

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main-arm64-default][biology/viennarna] Failed for viennarna-2.6.3 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-arm64-default/p85ccf094713a_sc584bb9cac1/logs/viennarna-2.6.3.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p85ccf094713a_sc584bb9cac1 Log: =>> Building biology/viennarna build started at Sat Sep 23…

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Bioconductor – Rnits

DOI: 10.18129/B9.bioc.Rnits   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Rnits. R Normalization and Inference of Time Series data Bioconductor version: 3.16 R/Bioconductor package for normalization, curve registration and inference in time course gene expression data. Author: Dipen P. Sangurdekar <dipen.sangurdekar at…

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How to fix `Exec /usr/local/bin/jupyterhub: exec format error`? – JupyterHub

I’m trying to deploy jupyterhub with helm. When I tried the default “k8s-hub:3.0.3” image hub: image: name: jupyterhub/k8s-hub tag: “3.0.3” It shows: File “<string>”, line 4, in <module> ModuleNotFoundError: No module named ‘kubernetes’ I found a solution from this. I went on and created a custom hub based on this…

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[Kernel-packages] [Bug 1988836] Autopkgtest regression report (linux-restricted-modules-azure/6.2.0-1013.13)

All autopkgtests for the newly accepted linux-restricted-modules-azure (6.2.0-1013.13) for lunar have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-525-server/525.125.06-0ubuntu0.23.04.1 (arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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View() shows blank pane in RStudio Desktop Pro 2023.06.2 – RStudio IDE

I installed RStudio Desktop Pro version 2023.06.2 yesterday, and now when I use View() I get a blank pane. Anyone else experiencing this? To repro: Open RStudio, run > x<-data.frame(x=runif(50)) > View(x) … observe that you get a blank pane showing no data. The same thing happens if I click…

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Building Pytorch – Missing Symbols – deployment

Cyberes September 7, 2023, 6:09am 1 I’m working on compiling PyTorch in my Dockerfile and running into a strange issue where the compiled libtorch.so only contains 4 symbols: ~ $ nm -D /opt/conda/lib/python3.9/site-packages/torch/lib/libtorch.so w _ITM_deregisterTMCloneTable w _ITM_registerTMCloneTable w __cxa_finalize w __gmon_start__ Compare that to the libtorch.so from pip: U __cxa_allocate_exception…

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CRAN Package Check Results for Package RSQLite

CRAN Package Check Results for Package RSQLite Last updated on 2023-09-07 11:53:17 CEST. Flavor Version Tinstall Tcheck Ttotal Status Flags r-devel-linux-x86_64-debian-clang 2.3.1 185.54 83.95 269.49 OK r-devel-linux-x86_64-debian-gcc 2.3.1 160.89 71.75 232.64 OK r-devel-linux-x86_64-fedora-clang 2.3.1 347.65 OK r-devel-linux-x86_64-fedora-gcc 2.3.1 434.27 OK r-devel-windows-x86_64 2.3.1 175.00 116.00 291.00 OK r-patched-linux-x86_64 2.3.1 193.84 80.73…

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Index of /ubuntu/ubuntu/pool/universe/g/golang-k8s-kube-openapi

Name Last modified Size Description Parent Directory   –   kube-openapi-dbgsym_0.0~git20211014.b3fe75c-2_amd64.ddeb 2021-11-09 06:39 4.4M   kube-openapi-dbgsym_0.0~git20211014.b3fe75c-2_arm64.ddeb 2021-11-09 06:40 4.0M   kube-openapi-dbgsym_0.0~git20211014.b3fe75c-2_armhf.ddeb 2021-11-09 06:40 3.9M   kube-openapi-dbgsym_0.0~git20211014.b3fe75c-2_ppc64el.ddeb 2021-11-09 06:39 4.0M   kube-openapi-dbgsym_0.0~git20211014.b3fe75c-2_riscv64.ddeb 2021-11-09 12:40 4.2M   kube-openapi-dbgsym_0.0~git20211014.b3fe75c-2_s390x.ddeb 2021-11-09 06:40 4.3M   kube-openapi-dbgsym_0.0~git20211014.b3fe75c-2ubuntu0.22.04.2_amd64.ddeb 2023-05-02 12:41 4.8M   kube-openapi-dbgsym_0.0~git20211014.b3fe75c-2ubuntu0.22.04.2_arm64.ddeb 2023-05-02 12:41 4.5M  …

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Trouble with breseq Bam2Cov

Hi All, and thank you for taking the time to try and help. I am using this pipeline to calculate the coverage of my sequencing across: You will need: Example install, how all of the above are installed: ./configure –prefix=/Path/to/new/folder I just called put in ./configure –prefix=/Users/phr361/tool cd tools_folder make…

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Leafcutter Installation Issue

Leafcutter Installation Issue 0 I keep trying to follow the installation instructions here. When I am doing the following: devtools::install_github(“davidaknowles/leafcutter/leafcutter”) I get the following error: fatal error: ‘tbb/task_scheduler_init.h’ file not found #include <tbb/task_scheduler_init.h> 22 warnings and 1 error generated. make: *** [stanExports_bb_glm.o] Error 1 ERROR: compilation failed for package ‘leafcutter’…

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How to install solo-sc or use hashsolo from scvi? – scvi-tools

When I attempt to install solo in conda environment lately, I have been encountering the following error. pip install solo-sc Collecting solo-sc Using cached solo-sc-1.3.tar.gz (18 kB) Preparing metadata (setup.py) … done Collecting ConfigArgParse (from solo-sc) Obtaining dependency information for ConfigArgParse from files.pythonhosted.org/packages/6f/b3/b4ac838711fd74a2b4e6f746703cf9dd2cf5462d17dac07e349234e21b97/ConfigArgParse-1.7-py3-none-any.whl.metadata Using cached ConfigArgParse-1.7-py3-none-any.whl.metadata (23 kB) Collecting pandas…

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Pytorch for Clara AGX – Holoscan SDK

Dear team, I am using Clara AGX with dGPU mode. And I am trying to install pytorch with GPU on it. I tried the following: Could not find a pytorch installer with GPU for arm64 on Pytorch’s website Installers from PyTorch for Jetson – Jetson & Embedded Systems / Jetson…

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rstudio-desktop PackagesNotFoundError: The following packages are not available from current channels – RStudio IDE

I recently got a new computer (MacBook Pro with Apple M2 Max chip). On my previous computer I installed and used RStudio fine in a conda environment using conda install -c conda-forge rstudio-desktop When I try this however, I get the message: PackagesNotFoundError: The following packages are not available from…

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Bugs : r-bioc-dada2 package : Ubuntu

$ remove-package -s mantic -m “Removed from Debian testing, blocking migration of r-bran-bh and r-bioc-dada2 (LP: #2030740)” q2-dada2Removing packages from mantic: q2-dada2 2022.11.2-2 in mantic  q2-dada2 2022.11.2-2 in mantic amd64Comment: Removed from Debian testing, blocking migration of r-bran-bh and r-bioc-dada2 (LP: #2030740)Remove [y|N]? y1 package successfully removed. $ remove-package -s mantic -m…

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Error starting RStudio 2023.06.01 on Macbook M1 2020 – RStudio IDE

System details RStudio Edition : Desktop RStudio Version : RStudio 2023.06.01 “Mountain Hydrangea” 547dcf86, 2023-07-06) for macOS OS Version : Ventura 13.4.1 – macOS – Apple Macbook Pro 13-inch M1, 2020 R Version : 4.3.1 (2023-06-16) — “Beagle Scouts”, Platform: x86_64-apple-darwin20 (64-bit) Steps to reproduce the problem I just downloaded…

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cp2k 2023.2 – Download, Browsing & More

cp2k 2023.2 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of cp2k-2023.2.tar.bz2 (27 Jul 10:02, 68243435 Bytes) About: CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material,…

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Using Bioconda with Mac M1 Processor?

Hello Everyone! I’m extremely new to bioinformatics, so please understand my complete ignorance to this process. My lab use to utilize Michigan States Ribosomal Database Project (RDP), but it recently stopped being supported and is no longer available. We are attempting to pivot to QIIME 2 to clean up and…

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Tljh compatibility with AWS Linux2 – The Littlest JupyterHub

A98 July 20, 2023, 9:52am 1 I have an “Amazon Linux2” server is it compatible to install jupyterhub? Do i follow the same steps as in Installing on your own server — The Littlest JupyterHub documentation to install jupyterhub on an existing ec2 instance? The needs are spelled out in…

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Leiden algorithm not working R studio scRNAseq

Hi, I would like to use the Leiden algorithm on my scRNAseq to identify the clusters but I cannot run the algorithm. If I use the default one I have no problem. I tried : FindClusters(immune.combined, resolution = 0.3, algorithm = 4) but it gives me this error: Error: Cannot…

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main-arm64-default][biology/mothur] Failed for mothur-1.48.0 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-arm64-default/p8fb94260154e_s510fd83138/logs/mothur-1.48.0.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p8fb94260154e_s510fd83138 Log: =>> Building biology/mothur build started at Mon Jul 17…

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r – Tesseract Package on Mac (RStudio): Installation Failure

I have installed Tesseract on Mac (Big Sur) using homebrew formulas. All dependencies are loaded. brew info tesseract ==> tesseract: stable 5.3.2 (bottled), HEAD OCR (Optical Character Recognition) engine github.com/tesseract-ocr/ /opt/homebrew/Cellar/tesseract/5.3.2 (73 files, 32.7MB) * Poured from bottle using the formulae.brew.sh API on 2023-07-16 at 21:46:16 From: github.com/Homebrew/homebrew-core/blob/HEAD/Formula/tesseract.rb License: Apache-2.0…

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main-arm64-default][biology/vcftools] Failed for vcftools-0.1.16 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: j…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-arm64-default/p8fb94260154e_s510fd83138/logs/vcftools-0.1.16.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p8fb94260154e_s510fd83138 Log: =>> Building biology/vcftools build started at Sat Jul 15…

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Generate download link MoThur APK

Device ID ABI Default arm64-v8a armeabi-v7a x86 x86_64 Device Default Phone Smart TV TV BOX Tablet SmartWatch Model Default Android DefaultAndroid 13Android 12+Android 12Android 11Android 10Android 9.0Android 8.1Android 8.0Android 7.1Android 7.0Android 6.0Android 5.1Android 5.0Android 4.4WAndroid 4.4Android…

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main-arm64-default][biology/clustalw] Failed for clustalw-2.1_2 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: j…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-arm64-default/p8fb94260154e_s510fd83138/logs/clustalw-2.1_2.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p8fb94260154e_s510fd83138 Log: =>> Building biology/clustalw build started at Fri Jul 14…

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Bug#1040964: src:slixmpp: fails to migrate to testing for too long: autopkgtest regression

Source: slixmpp Version: 1.8.3-1 Severity: serious Control: close -1 1.8.4-2 Tags: sid trixie User: release.debian….@packages.debian.org Usertags: out-of-sync Control: block -1 by 1040057 Dear maintainer(s), The Release Team considers packages that are out-of-sync between testing and unstable for more than 30 days as having a Release Critical bug in testing [1]….

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Page Not Found – Image.sc Forum

Sign Up Log In Log In Popular Qupath extension Segment Anything Model (SAM)Announcements Cellsparse: Training deep learning models for cell image segmentation with sparse annotationsAnnouncements Request for testing: napari 0.4.18 release candidateAnnouncements Ome-types rewritten, requesting alpha testersAnnouncements Noise in fluorescence imagesImage Analysis Visualisation of spatial-omics dataImage Analysis Introducing the Java…

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Bug#1034348: at: autopkgtest regression on arm64

Dear maintainer(s), I saw the autoremoval notice for 11th July on the Debian Package Tracker. Hope this is the right place to respond. I use `at` regularly and would be sad to see it being removed from the Debian repositories. Unfortunately I have not been able to reproduce this issue…

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[Kernel-packages] [Bug 2024675] Autopkgtest regression report (nvidia-graphics-drivers-525/525.125.06-0ubuntu0.22.10.1)

All autopkgtests for the newly accepted nvidia-graphics-drivers-525 (525.125.06-0ubuntu0.22.10.1) for kinetic have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-515/515.105.01-0ubuntu0.22.10.1 (amd64, arm64) nvidia-graphics-drivers-525/525.125.06-0ubuntu0.22.10.1 (amd64, arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding…

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Rocker Project – Other projects

Here are some images and tools that serve a similar purpose to the Rocker images. Please refer to the links for more information. Docker images for R Jupyter Docker Stacks The stack of Docker images by Project Jupyter, based on Ubuntu, install packages from conda-forge, and configured to run Jupyter….

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Bugs : python-reportlab package : Ubuntu

Removal request————— Please remove the old python3-renderpm & python3-reportlab-accel binaries built from src:python-reportlab for any architecture from Mantic. The binary packages are:python3-renderpm 3.6.13-1python3-reportlab-accel 3.6.13-1 Those binary packages got dropped by the Debian maintainer in 4.0.4-1https://bugs.debian.org/1037483 Additional information:A few reverse-depends are affected, which should be handled individually: $ reverse-depends python3-renderpm -r…

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Laptops for bioinformatics

I have seen a lot of misinformation in this thread about Mac M1 systems. I feel the need to address these as an new answer rather than a comment. First, I have yet to see a command line tool that did not run on M1. Perhaps those with GUIs do…

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Bioconductor – gDRtestData (development version)

DOI: 10.18129/B9.bioc.gDRtestData   This is the development version of gDRtestData; to use it, please install the devel version of Bioconductor. gDRtestData – R data package with testing dose reponse data Bioconductor version: Development (3.18) R package with internal dose-response test data. Package provides functions to generate input testing data that…

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Stream RStudio: A Powerful IDE for R Programming on macOS from Ofysimidydy1975

published on 2023-06-22T19:08:37Z r studio download mac Download climmulponorc.blogspot.com/?c=2uocTB R is maintained by an international team of developers who make the language available through the web page of The Comprehensive R Archive Network. The top of the web page provides three links for downloading R. Follow the link that describes…

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macos – Cant install R-bioconductor-packages via anaconda

I wanted to start using conda evironments on my new computer, primarily for bioinformatic analysis. However, I can not bring it to download bioconductor packages. I tried several approaches right now, but could not accomplish a succesful installation. Installation I basically followed the instructions on this website Starting by downlaoding…

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Compile gromacs with nvhpc 23.5 on arm64 – nvc, nvc++ and nvfortran

I am trying to build gromacs 22.4 with nvhpc 23.5 on arm64 and run into the following error (related to int64_t). Is there any walk around this? cd /shared/tools/gromacs-2022.4/build_mpi-nvhpc/src/gromacs && /shared/nvidia/hpc_sdk/Linux_aarch64/23.5/comm_libs/mpi/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DMUPARSER_STATIC -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/shared/tools/gromacs-2022.4/src/include -I/shared/tools/gromacs-2022.4/build_mpi-nvhpc/src/include -I/shared/tools/gromacs-2022.4/src -I/shared/tools/gromacs-2022.4/api/legacy/include -I/shared/tools/gromacs-2022.4/build_mpi-nvhpc/api/legacy/include -I/shared/tools/gromacs-2022.4/src/gromacs/analysisdata/include -I/shared/tools/gromacs-2022.4/src/gromacs/utility/include -I/shared/tools/gromacs-2022.4/src/gromacs/applied_forces/include -I/shared/tools/gromacs-2022.4/src/gromacs/commandline/include -I/shared/tools/gromacs-2022.4/src/gromacs/compat/include -I/shared/tools/gromacs-2022.4/src/gromacs/coordinateio/include -I/shared/tools/gromacs-2022.4/src/gromacs/correlationfunctions/include -I/shared/tools/gromacs-2022.4/src/gromacs/domdec/include…

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Michigan Imputation Server – Local docker image

Michigan Imputation Server – Local docker image 0 Hi, Due to clinical data and not meeting the minimum sample of 20, I hope to use the Michigan Imputation Server locally via its’ Docker image. I got couple of questions that I hope others can help: I tried to do this…

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Bug#1033907: numba: autopkgtest regression: segmentation fault on arm64

I’m not really sure what to do about it. I looked some and there are a variety of different types of segfaults triggered by numba on arm64. I wasn’t able to find any particular patterns. I have most of the patches they initially recommended but upstream has moved on to released 0.57.0 which…

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How to check and change the default device to MPS in PyTorch

This post will talk about GPU-accelerated PyTorch training using the MPS backend on Mac platforms. MPS enables high-performance training on GPU for MacOS devices with a Metal programming framework. I’ll also provide an overview of the software stack. So let’s talk briefly about the MPS backend and software components it…

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BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3)

BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3) 0 @mjsteinbaugh Last seen 23 hours ago Cambridge, MA Hi Bioconductor team, I’m seeing a warning pop up during BiocManager::install calls on Apple Silicon related to the current BioCann repository index configuration. BiocManager::repositories() BioCsoft “https://bioconductor.org/packages/3.17/bioc” BioCann “https://bioconductor.org/packages/3.17/data/annotation” BioCexp…

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Error building package: graph from Bioconductor – shinyapps.io

Dear all,I come to a point where I need help. I am trying to deploy a shiny app and obtain the error below: Preparing to deploy document…DONEUploading bundle for document: 8572645…DONEDeploying bundle: 7200847 for document: 8572645 …Waiting for task: 1299182367building: Building image: 8559204building: Installing system dependenciesbuilding: Fetching packageserror: Building package:…

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CRAN – Package ggplot2.utils

ggplot2.utils: Selected Utilities Extending ‘ggplot2’ Selected utilities, in particular ‘geoms’ and ‘stats’ functions, extending the ‘ggplot2’ package. Note that this package does not define the functions itself, but instead imports them from a collection of other packages and then exports them. These functions are tested as well to make sure…

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[Kernel-packages] [Bug 2018226] Autopkgtest regression report (dkms/3.0.10-7ubuntu1)

All autopkgtests for the newly accepted dkms (3.0.10-7ubuntu1) for lunar have finished running. The following regressions have been reported in tests triggered by the package: acpi-call/1.2.2-2.1 (armhf, ppc64el, s390x) backport-iwlwifi-dkms/9904-0ubuntu5 (s390x) dahdi-linux/1:2.11.1.0.20170917~dfsg-8.4ubuntu1 (s390x) ddcci-driver-linux/0.4.2-4 (s390x) librem-ec-acpi/0.9.1-4ubuntu1 (armhf, ppc64el, s390x) openrazer/3.4.0+dfsg-1ubuntu1 (s390x) rtl8812au/4.3.8.12175.20140902+dfsg-0ubuntu19 (s390x) v4l2loopback/0.12.7-2ubuntu3 (s390x) xilinx-runtime/2.8.743-0ubuntu9 (arm64) Please visit the…

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Bioconductor – Bioconductor 3.17 Released

Home Bioconductor 3.17 Released April 26, 2023 Bioconductors: We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books. There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows,…

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RStudio Desktop Pro for Ubuntu 22 (arm64)

These builds use your existing license. If you haven’t yet licensed the product then the build provides a 45-day evaluation version subject to the Posit End User License Agreement. By downloading the product you acknowledge that you either have an existing license or that you are evaluating the product and…

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BLAS not shown in `sessionInfo()` output in RStudio – RStudio IDE

The BLAS matrix product is not listed in the sessionInfo() output if run in RStudio from an R script or the console pane, but it is listed if run in an R session in the terminal/command line. It is also listed if rendered by rmarkdown or reprex. From the RStudio…

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Either at.20377 doesn’t exist or the content differs.

Source: at Version: 3.2.5-1 Severity: serious Control: tags -1 bookworm-ignore User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails on arm(64|el|hf) since September 2022 (and slightly longer on s390x). Can you please investigate the situation and fix it? I copied some of the output…

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Bug#1034350: gnutls28: autopkgtest regression everywhere except amd64: src/nonexist-builddir/gnutls_ktls: not found

On 2023-04-13 Paul Gevers <elb…@debian.org> wrote: > Source: gnutls28 > Version: 3.7.9-1 > Severity: serious > Control: tags -1 bookworm-ignore > User: debi…@lists.debian.org > Usertags: regression > Dear maintainer(s), > Your package has an autopkgtest, great. However, it fails everywhere but on > amd64. If I understand correctly, the 32 bits…

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Bug#1034352: golang-github-azure-go-autorest: autopkgtest regression on arm64: request header doesn’t match

Source: golang-github-azure-go-autorest Version: 14.2.0+git20220726.711dde1-1 Severity: serious Control: tags -1 bookworm-ignore User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails on arm64 only since July 2022. Can you please investigate the situation and fix it? I copied some of the output at the bottom of…

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all warnings being treated as errors

Source: libcereal Version: 1.3.2+dfsg-4 Severity: serious Control: tags -1 bookworm-ignore User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails on all architectures except amd64 and i386 since August 2022. Can you please investigate the situation and fix it? I copied some of the output…

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times out when run on bookworm kernel

Source: accountsservice Version: 22.08.8-6 Severity: serious Control: tags -1 bookworm-ignore User: debian…@lists.debian.org Usertags: timeout Dear maintainer(s), Your package has an autopkgtest, great. However, it fails when run on a bookworm kernel. Last month I started to upgrade the workers of ci.debian.net on some architectures. The architectures that I upgraded now…

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Bug#1034030: rust-async-stream: autopkgtest regression: error[E0658]: yield syntax is experimental

Source: rust-async-stream Version: 0.3.3-1 Severity: serious Control: tags -1 bookworm-ignore User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails since December 2022. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. The…

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ruby-rails-assets-fine-uploader: autopkgtest regression: Don’t know how to build task ‘assets:precompile’

Source: ruby-rails-assets-fine-uploader Version: 5.13.0-2 Severity: serious Control: tags -1 bookworm-ignore sid bookworm User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails since November 2021. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this…

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Cannot set locale in Rstudio

## — The problem: — I’m trying to run Rstudio, but whenever I start up I see these messages: During startup – Warning messages: 1: Setting LC_CTYPE failed, using “C” 2: Setting LC_COLLATE failed, using “C” 3: Setting LC_TIME failed, using “C” 4: Setting LC_MONETARY failed, using “C” Which I…

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Bug#1033711: kore: autopkgtest regression: Killing leaked background processes

Source: kore Version: 4.1.0-6 Severity: serious Control: tags -1 bookworm-ignore User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails since May 2022. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. The…

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Bug#1033824: passwordsafe: autopkgtest regression: test dependencies transitioned

Source: passwordsafe Version: 1.16.0+dfsg-1 Severity: serious Control: tags -1 bookworm-ignore User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it started to fail when we finished the wcwidgets3.0 -> wxwidgets3.2 transition in January 2023. Can you please investigate the situation and fix it? I copied some…

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Gene duplicate

Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…

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