Tag: arm64

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…

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…

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…

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…

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:…

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…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

## — 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…

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…

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…

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…

All autopkgtests for the newly accepted systemd (245.4-4ubuntu3.21) for focal have finished running. The following regressions have been reported in tests triggered by the package: apt/2.0.9 (armhf) bilibop/unknown (s390x) freeipa/unknown (s390x) fwupd/1.7.9-1~20.04.1 (armhf) libsoup2.4/2.70.0-1 (s390x) libusb-1.0/unknown (s390x) libvirt/unknown (s390x) linux-aws-5.11/blacklisted (amd64, arm64) linux-aws-5.13/blacklisted (amd64, arm64) linux-aws-5.15/5.15.0-1033.37~20.04.1 (arm64) linux-aws-5.15/unknown (amd64) linux-aws-5.8/blacklisted…

Dear CP2K developers,    I was trying to compile the latest version of CP2K (CP2K2023.1) using NVIDIA’s NVHPC compiler set, but ran into the following error messages: NVFORTRAN-S-0155-PASS argument must be declared CLASS in mp_irecv_custom (/home/chenhanning/Downloads/cp2k/src/mpiwrap/message_passing.F: 4769)NVFORTRAN-S-0155-PASS argument name/position must match parent’s PASS argument name/position in type bound procedure mp_irecv_custom…

Go up — — python3-sage_9.5-4+b3_amd64.deb 40 MiB 07/16/2022 06:56:00 AM +00:00 python3-sage_9.5-4+b3_arm64.deb 37 MiB 07/16/2022 08:57:18 AM +00:00 python3-sage_9.5-4+b3_i386.deb 41 MiB 07/16/2022 07:41:25 AM +00:00 python3-sage_9.5-6_amd64.deb 40 MiB 02/07/2023 07:28:01 PM +00:00 python3-sage_9.5-6_arm64.deb 37 MiB 02/07/2023 08:18:53 PM +00:00 python3-sage_9.5-6_i386.deb 41 MiB 02/07/2023 07:27:57 PM +00:00 sagemath-doc_9.5-6_all.deb 71 MiB 02/07/2023…

Source: chromhmm X-Debbugs-Cc: vladimi…@canonical.com Version: 1.24+dfsg-1 Severity: normal $sudo apt install chromhmm Reading package lists… Done Building dependency tree… Done Reading state information… Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been…

mcrotti1 (Mcrotti1) February 24, 2023, 10:24am 1 Hello, I have a question related to building containers for multi architectures.I am working from a mac the the M1 arm chip. Usually, I write my docker file and use the commanddocker buildx build –platform linux/arm64,linux/amd64 -t name:latest –push .And this works fine,…

take0 February 23, 2023, 11:49am 1 I have set up Orin as follows $ sudo bash -c ‘echo “deb repo.download.nvidia.com/jetson/common r34.1 main” >> /etc/apt/sources.list.d/nvidia-l4t-apt-source.list’ $ sudo apt update $ sudo apt upgrade $ sudo apt install nvidia-jetpack $ sudo apt-get -y install autoconf bc build-essential g++-8 gcc-8 clang-8 lld-8 gettext-base…

Source: rust-typenumVersion: 1.16.0-1Severity: serious tracker.debian.org/pkg/rust-typenum …Issues preventing migration:∙ ∙ autopkgtest for rust-typenum/1.16.0-1: amd64: Pass, arm64: Pass, armel: Regression ♻ (reference ♻), armhf: Regression ♻ (reference ♻), i386: Regression ♻ (reference ♻), ppc64el: Pass, s390x: Pass ci.debian.net/data/autopkgtest/testing/armhf/r/rust-typenum/31550189/log.gz …error[E0119]: conflicting implementations of trait `generated::generic_const_mappings::ToUInt` for type `generated::generic_const_mappings::Const<0_usize>`–> /tmp/tmp.OgQsyeMSQY/target/armv7-unknown-linux-gnueabihf/debug/build/typenum-fe1e7c2e1c5cb87d/out/generic_const_mappings.rs:4245:5|61 | impl ToUInt for…

Hi, thank you for your reply. I’m not from programming background and trying to self learn bioinformatics, so I don’t know the exact problem. I will try to be more descriptive this time. When I use conda install -c conda-forge ambertools It gives me error for package. Which I see…

All autopkgtests for the newly accepted linux-meta-lowlatency-hwe-5.15 (5.15.0.66.73~20.04.24) for focal have finished running. The following regressions have been reported in tests triggered by the package: linux-lowlatency-hwe-5.15/5.15.0-66.73~20.04.1 (arm64) dpdk/19.11.13-0ubuntu0.20.04.1 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…

Hi, I have installed pytorch on my Xavier NX from developer.download.nvidia.cn/compute/redist/jp/v51/pytorch/torch-1.14.0a0+44dac51c.nv23.01-cp38-cp38-linux_aarch64.whl. However, when I import torch, I receive the following exception Traceback (most recent call last): File “<stdin>”, line 1, in <module> File “/data/cascade-st/venv/lib/python3.8/site-packages/torch/__init__.py”, line 192, in <module> _load_global_deps() File “/data/cascade-st/venv/lib/python3.8/site-packages/torch/__init__.py”, line 154, in _load_global_deps ctypes.CDLL(lib_path, mode=ctypes.RTLD_GLOBAL) File “/home/dev/.pyenv/versions/3.8.15/lib/python3.8/ctypes/__init__.py”, line…

Hi, I failed to install clusterProfiler on Mac M1. May I ask the solution >BiocManager::install(“clusterProfiler”) Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) ‘clusterProfiler’ also installing the dependencies ‘fgsea’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’ Warning: unable to access index for repository bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL ‘https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES’ Warning: unable to access…

Source: espeak-ng Version: 1.51+dfsg-9 Severity: serious tags: patch Hello, autopkgtests started to fail I presume since llvm-default change. To fix, you need to depend on clang-rt when you use fsanitize=fuzzer) clang++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/tmp/autopkgtest-lxc.4x6n726o/downtmp/build.8AY/src=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tests/dummy.o tests/dummy.cpp /bin/bash ./libtool –tag=CXX –mode=link clang++…

Source: davmail Version: 6.0.1.3390-5 Severity: serious User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of davmail the autopkgtest of davmail fails in testing when that autopkgtest is run with the binary packages of davmail from unstable on arm64, armhf and ppc64el. It passes when run with only packages…

Hi, when I try to install Bioconductor package ‘affy’ Experience below error\ May I know how do I fix this? I’m currently using R4.2.2 on MacBook Air, M1\ R version 4.2.2 (2022-10-31) — “Innocent and Trusting”\ Copyright (C) 2022 The R Foundation for Statistical Computing\ Platform: aarch64-apple-darwin20 (64-bit) BiocManager::install(“affy”) ‘getOption(“repos”)’…

I am a relatively new R-user. I am currently working on trying to read .maf files via the maftools package released by Bioconductor. I am following the instructions as posted on the Bioconductor website (www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#4_Installation), however, everytime I attempt to run the installation, it gets stuck on RSQLite and I…

This is where the installation failed. I tried installing DESeq2 on “R Studio Cloud” and it worked. I am assuming this is a mac issue. If anyone knows what to do I would very much appreciate it! Very new to R so anything will help. make: /opt/R/arm64/bin/gfortran: No such file…

otrujillor (Otrujillor) October 5, 2022, 5:11am #1 Is there any way to analyze the microbiome functionality with QIIME2.I have the following files: metadata.tsv the forward reads (****_L001_R1_001.fastq.gz) the reverse reads (****_L001_R2_001.fastq.gz) And I have already imported my data into QIIME2 and got the *.qza file.I performed the sequence quality control…

T.Dem June 25, 2022, 5:41pm #1 Dear LAMMPS users, I am trying to run Monte Carlo simulations using reaxff to study the oxygen coverage on a Pt nanoparticle. I defined my oxygen reservoir using the chemical potential definition for a perfect gas. Initially, the system is very small (350 atoms)…

Hi Uri, Thank you for the patch! Yet something to improve: [auto build test ERROR on staging/staging-testing] url: github.com/intel-lab-lkp/linux/commits/Uri-Arev/staging-fbtft-fix-checkpatch-pl-struct-should-normally-be-const/20220520-012948 base: git.kernel.org/pub/scm/linux/kernel/git/gregkh/staging.git 4d0cc9e0e53e9946d7b8dc58279c62dfa7a2191b config: arm64-randconfig-r011-20220519 (download.01.org/0day-ci/archive/20220520/202205200821.nJQ0IfFt-lkp@xxxxxxxxx/config) compiler: clang version 15.0.0 (github.com/llvm/llvm-project e00cbbec06c08dc616a0d52a20f678b8fbd4e304) reproduce (this is a W=1 build): wget raw.githubusercontent.com/intel/lkp-tests/master/sbin/make.cross -O ~/bin/make.cross chmod +x ~/bin/make.cross # install arm64 cross compiling tool…

All autopkgtests for the newly accepted linux-meta (5.15.0.28.31) for jammy have finished running. The following regressions have been reported in tests triggered by the package: oss4/4.2-build2010-5ubuntu9 (amd64) network-manager/1.36.4-2ubuntu1 (ppc64el, arm64, amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding…

Mohammed Guys, does anyone know the answer? get which of the following are the prerequisite packages for scikit-learn? from screen. Installing scikit There are different ways to install scikit-learn: Install the latest official release. This is the best approach for most users. It will provide a stable version and pre-built…

All autopkgtests for the newly accepted glibc (2.31-0ubuntu9.9) for focal have finished running. The following regressions have been reported in tests triggered by the package: hilive/2.0a-3build2 (arm64) tomb/2.7+dfsg2-1 (arm64) linux-hwe-5.13/5.13.0-40.45~20.04.1 (armhf) bali-phy/3.4.1+dfsg-2build1 (s390x, arm64) smalt/0.7.6-9 (ppc64el) mariadb-10.3/1:10.3.34-0ubuntu0.20.04.1 (armhf) feersum/1.407-2 (s390x) kopanocore/8.7.0-7ubuntu1 (amd64) r-cran-ps/1.3.2-2 (s390x, ppc64el) libreoffice/1:6.4.7-0ubuntu0.20.04.4 (amd64) imagemagick/8:6.9.10.23+dfsg-2.1ubuntu11.4 (armhf) ruby-stackprof/0.2.15-2…

All autopkgtests for the newly accepted docker.io (20.10.12-0ubuntu2~20.04.1) for focal have finished running. The following regressions have been reported in tests triggered by the package: golang-github-fsouza-go-dockerclient/1.6.0-2 (arm64, amd64, ppc64el, s390x, armhf) golang-github-openshift-imagebuilder/1.1.0-2 (arm64, amd64, ppc64el, s390x, armhf) ubuntu-fan/0.12.13 (arm64, amd64, ppc64el, s390x) Please visit the excuses page listed below and…

#1007013 – freecad: autopkgtest regression on arm64 and armhf: syntax error – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>:Bug#1007013; Package src:freecad. (Thu, 10 Mar 2022 14:21:07 GMT) (full text, mbox, link). Acknowledgement sent to Paul Gevers…

I wanted to install the sklearn package in PyCharm. However, I always got the same error (below is an extract): pip install scikit-learn # input Collecting scikit-learn Using cached scikit-learn-1.0.2.tar.gz (6.7 MB) Installing build dependencies … error error: subprocess-exited-with-error × pip subprocess to install build dependencies did not run successfully….

I am trying to use Biopython using anaconda and the Jupiter notebook with Python3. However, simply import numpy gives the following error: ————————————————————————— ImportError Traceback (most recent call last) File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/__init__.py:23, in <module> 22 try: —> 23 from . import multiarray 24 except ImportError as exc: File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/multiarray.py:10, in <module>…

Hardware Pre-requisite Jetson Nano A 5V 4Ampere Charger 64GB SD card Software Preparing Your Raspberry Pi Flashing Jetson SD Card Image Unzip the SD card image Insert SD card into your system. Bring up Etcher tool and select the target SD card to which you want to flash the image….

Warning messages on Apple M1 BigSur 0 @095e334e Last seen 4 hours ago Hong Kong Hi, Does bioconductor supports the binary of R created specifically for arm chips already ? I get the following warning when trying to install any Bioconductor packages: 1: In .inet_warning(msg) : unable to access index…

error: cannot execute ‘f951’: execvp: No such file or directory when downloading DESeq2 package 0 @8e03f28b Last seen 4 hours ago United States When I download a package (DESeq2) from Bioconductor, I got the following error: gfortran: fatal error: cannot execute ‘f951’: execvp: No such file or directory compilation terminated….

install GenomicFeatures fail 1 @5b9023e7 Last seen 19 hours ago China BiocManager::install(‘GenomicFeatures’) results show ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) ‘GenomicFeatures’ also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’ Packages which are only…

Issue with Seurat SpatialPlot: spots not filling the whole tissue image 0 In Seurat, SpatialPlot generates a plot with an enlarged/expanded image of tissue section as compared to the original spot image. This seems to happen on the relatively small image with a number of spots around 500. I ‘d…