Tag: GNU

Ubuntu Manpage: Bio::Roary::External::Makeblastdb – Wrapper around NCBIs makeblastdb command

Provided by: roary_3.13.0+dfsg-1_all NAME Bio::Roary::External::Makeblastdb – Wrapper around NCBIs makeblastdb command VERSION version 3.13.0 SYNOPSIS Take in a fasta file and create a temporary blast database. use Bio::Roary::External::Makeblastdb; my $blast_database= Bio::Roary::External::Makeblastdb->new( fasta_file => ‘contigs.fa’, exec => ‘makeblastdb’ ); $blast_database->run(); METHODS output_database Returns the path to the temporary blast database files…

Continue Reading Ubuntu Manpage: Bio::Roary::External::Makeblastdb – Wrapper around NCBIs makeblastdb command

rstudio – Cannot deploy R-shiny app due to “fribidi was not found”

Local app runs fine, but I keep encountering this error when attempting to publish it. I have already installed fribidi & harfbuzz using brew install fribidi & brew install harfbuzz on my Mac, but I am still encountering the error. I am using: Installing urltools (1.7.3) … Using cached urltools….

Continue Reading rstudio – Cannot deploy R-shiny app due to “fribidi was not found”

Debian — File list of package slurm-wlm-mysql-plugin/sid/riscv64

/usr/lib/riscv64-linux-gnu/slurm-wlm/accounting_storage_mysql.so /usr/lib/riscv64-linux-gnu/slurm-wlm/jobcomp_mysql.so /usr/share/doc/slurm-wlm-mysql-plugin/changelog.Debian.gz /usr/share/doc/slurm-wlm-mysql-plugin/copyright /usr/share/lintian/overrides/slurm-wlm-mysql-plugin /usr/lib/riscv64-linux-gnu/slurm-wlm/accounting_storage_mysql.so /usr/lib/riscv64-linux-gnu/slurm-wlm/jobcomp_mysql.so /usr/share/doc/slurm-wlm-mysql-plugin/changelog.Debian.gz /usr/share/doc/slurm-wlm-mysql-plugin/copyright /usr/share/lintian/overrides/slurm-wlm-mysql-plugin Read more here: Source link

Continue Reading Debian — File list of package slurm-wlm-mysql-plugin/sid/riscv64

Installation with GPU – User discussions

GROMACS version: 2023.3GROMACS modification: Yes/NoHere post your question Im trying to install gromacs with SYCL GPU suport using $ cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=SYCL -DGMX_SYCL_HIPSYCL=on but I got the error CMake Error at cmake/gmxManageSYCL.cmake:77 (message):HipSYCL build requires Clang compiler, but GNU is usedCall Stack (most recent call first):CMakeLists.txt:667 (include) and…

Continue Reading Installation with GPU – User discussions

Update to (git-version 2.0.1 revision commit).

* gnu/packages/bioinformatics.scm (r-sccustomize): Update to (git-version 2.0.1 revision commit). Change-Id: I4e4b499a658eaed0396263d1d9fd277a541a13d9 — gnu/packages/bioinformatics.scm | 87 ++++++++++++++++—————– 1 file changed, 43 insertions(+), 44 deletions(-) Toggle diff (108 lines) diff –git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2546454acd..3e7b99ee61 100644 — a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10245,55 +10245,54 @@ (define-public r-presto (license license:gpl3)))) (define-public r-sccustomize – (let…

Continue Reading Update to (git-version 2.0.1 revision commit).

132releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.1.1_1 in configure

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/132releng-armv7-default/1dd4264fe4a8/logs/py39-pytorch-2.1.1_1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=132releng-armv7-default&build=1dd4264fe4a8 Log: =>> Building misc/py-pytorch build started at Tue Dec 19…

Continue Reading 132releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.1.1_1 in configure

Accepted r-bioc-genomeinfodb 1.38.2+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 18 Dec 2023 13:36:52 +0100 Source: r-bioc-genomeinfodb Architecture: source Version: 1.38.2+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-genomeinfodb (1.38.2+dfsg-1) unstable; urgency=medium . * New upstream version Set upstream metadata fields: Archive….

Continue Reading Accepted r-bioc-genomeinfodb 1.38.2+dfsg-1 (source) into unstable

drivers/power/wm97xx_battery.c – kernel/tegra.git – Git at Google

/* * linux/drivers/power/wm97xx_battery.c * * Battery measurement code for WM97xx * * based on tosa_battery.c * * Copyright (C) 2008 Marek Vasut <marek.vasut@gmail.com> * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License version 2 as…

Continue Reading drivers/power/wm97xx_battery.c – kernel/tegra.git – Git at Google

Image:Gengis Khan empire-fr.svg – from the Schools Wikipedia

From Wikipedia, the free encyclopedia This is a file from the Wikimedia Commons. The description on its description page there is shown below.Commons is a freely licensed media file repository. You can help. Description Français : Carte de l’empire mongol au XIIIème siècle English: Genghis Khan empire, XIIIth century Source Own…

Continue Reading Image:Gengis Khan empire-fr.svg – from the Schools Wikipedia

Installing JupyterHub via Stackable Demo on K8s | by Alex McLintock | Dec, 2023

docs.stackable.tech/home/stable/demos/jupyterhub-pyspark-hdfs-anomaly-detection-taxi-data So, this is an article in an ongoing series where I investigate the deployment tools of Stackable.tech This firm supplies supported versions of many open source data engineering tools to easily build data platforms on Kubernetes (k8s) clusters. These can be on your own premises, in a data centre,…

Continue Reading Installing JupyterHub via Stackable Demo on K8s | by Alex McLintock | Dec, 2023

[llvm-bugs] [Bug 75428] clang crash when build IPEX code.

Issue 75428 Summary clang crash when build IPEX code. Labels clang Assignees Reporter xuhancn The error msg: “`cmd Stack dump: 0. Program arguments: /usr/bin/clang++ -DAT_PARALLEL_OPENMP=1 -DUSE_C10D_GLOO -DUSE_DISTRIBUTED -DUSE_RPC -DUSE_TENSORPIPE -Dintel_ext_pt_cpu_EXPORTS -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/aten -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/tpp -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/libxsmm/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/build/Release/csrc/cpu/csrc/cpu/cpu_third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/include -I/home/xu/anaconda3/envs/ipex_cpu/include/python3.12 -I/home/xu/anaconda3/envs/ipex_cpu/include -I/home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include/torch/csrc/api/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/src/../include -isystem /home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include -fPIC…

Continue Reading [llvm-bugs] [Bug 75428] clang crash when build IPEX code.

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…

Continue Reading autopkgtest regression on architectures where char is unsigned

Bioconductor Code: plier

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. Copyright (C) 2004 Affymetrix, Inc. and Paterson Institute for Cancer Research UK This program is free…

Continue Reading Bioconductor Code: plier

Accepted r-bioc-rgsepd 1.34.0-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 08 Dec 2023 16:06:05 +0100 Source: r-bioc-rgsepd Architecture: source Version: 1.34.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-rgsepd (1.34.0-1) unstable; urgency=medium . * New upstream version * Add d/t/autopkgtest-pkg-r.conf Checksums-Sha1: a9877c97580151121f8e6a6ac5425b3814c4c6f0…

Continue Reading Accepted r-bioc-rgsepd 1.34.0-1 (source) into unstable

Rstudio cloud

Rstudio cloud 1 Dear fellows, a bit off topic today. I am just starting to use R studio cloud from a supercomputer to analyze my single cell and have recently experienced issue with installing packages. Not sure whether anyone have any experience installing packages in R studio cloud and could…

Continue Reading Rstudio cloud

Bioconductor Code: CelliD

# CelliD v0.99 R package for gene signature extraction and cell identity recognition at individual cell level from single-cell RNA-seq. ![logo](https://github.com/RausellLab/CelliD/blob/gh-pages/tools/sticker.png?raw=true) —————————————- Welcome to the official Github repository of the **CelliD** software presented in the Article [Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID, Nature…

Continue Reading Bioconductor Code: CelliD

Bioconductor – DropletUtils

DOI: 10.18129/B9.bioc.DropletUtils     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DropletUtils. Utilities for Handling Single-Cell Droplet Data Bioconductor version: 3.15 Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data…

Continue Reading Bioconductor – DropletUtils

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…

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

Accepted r-bioc-scrnaseq 2.16.0+ds-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 01 Dec 2023 16:47:13 +0100 Source: r-bioc-scrnaseq Architecture: source Version: 2.16.0+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-scrnaseq (2.16.0+ds-1) unstable; urgency=medium . * Team upload. * New upstream version Checksums-Sha1: 886053d20feab7314d553249e052d3bbcc1e0d28…

Continue Reading Accepted r-bioc-scrnaseq 2.16.0+ds-1 (source) into unstable

RStudio doesn’t work on Debian 12 with R version 4.3.2 – General

Hello, From the download website, it seems RStudio support Debian 12. I have installed R 4.3.2 R version 4.3.2 (2023-10-31) — “Eye Holes”Copyright (C) 2023 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain…

Continue Reading RStudio doesn’t work on Debian 12 with R version 4.3.2 – General

Accepted r-bioc-goseq 1.54.0-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 01 Dec 2023 11:53:07 +0100 Source: r-bioc-goseq Architecture: source Version: 1.54.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-goseq (1.54.0-1) unstable; urgency=medium . * New upstream version * Add d/t/autopkgtest-pkg-r.conf Checksums-Sha1: 9a60c9189f597ab34494ac9006a997cc48bcb38f…

Continue Reading Accepted r-bioc-goseq 1.54.0-1 (source) into unstable

Why is DMRcate not available for Bioconductor version 3.18?

Why is DMRcate not available for Bioconductor version 3.18? 0 @daniel-e-weeks-10677 Last seen 22 hours ago Pittsburgh, Pennsylvania, United States… According to the Bioconductor web page for DMRcate, it looks like it is available for Bioconductor version 3.18 but this installation fails: > BiocManager::install(“DMRcate”) Bioconductor version 3.18 (BiocManager 1.30.22), R…

Continue Reading Why is DMRcate not available for Bioconductor version 3.18?

Dryad | Data — Progressive Cactus alignment of 298 drosophilid species

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. Whole-genome sequence alignments link evolution at the nucleotide level across species and are a critical but computationally intensive step for…

Continue Reading Dryad | Data — Progressive Cactus alignment of 298 drosophilid species

Which program, tool, or strategy do you use to visualize genomic rearrangements?

Which program, tool, or strategy do you use to visualize genomic rearrangements? 5 Which program, tool, or strategy do you use to visualize genomic rearrangements? In relation to my master thesis I’m working on tools to visualize fusion genes. In that regard I’m interested in any and all strategies and…

Continue Reading Which program, tool, or strategy do you use to visualize genomic rearrangements?

Simulation & CAE Software Industry Data and In-depth Analysis to 2029

Global Market Vision published a new industry research that focuses on Global Simulation & CAE Software Market and delivers in-depth market analysis and future prospects of Global Simulation & CAE Software Market. The study covers significant data which makes the research document a handy resource for managers, analysts, industry experts…

Continue Reading Simulation & CAE Software Industry Data and In-depth Analysis to 2029

20 Best Neural Network Software for 2024

Image: Siarhei/Adobe Stock eWEEK content and product recommendations are editorially independent. We may make money when you click on links to our partners. Learn More. Neural network software enables the implementation, deployment and training of artificial neural networks. These networks are designed to mimic the behavior of the human brain…

Continue Reading 20 Best Neural Network Software for 2024

Problem in installing ‘magick’ R package

Problem in installing ‘magick’ R package 0 Hi everyone: I have attempted to install the R package ‘magick’ on R (version: 4.3.1) using the following command: install.packages(“magick”) However, it turns out that there were some warning messaged popped out in the R console: Installing package into ‘/home/billychan/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is…

Continue Reading Problem in installing ‘magick’ R package

linux – cannot install R package in Rstudio cloud

I am just starting using Rstudio Cloud in Linux and encountered issue installing the package. I just started with tidyverse #install tidyverse packages options(repos = c(CRAN = “https://cloud.r-project.org”)) options(download.file.method = “libcurl”) install.packages(“tidyverse”) #Error I got > install.packages(“tidyverse”) Warning in install.packages : unable to access index for repository cloud.r-project.org/src/contrib: cannot open…

Continue Reading linux – cannot install R package in Rstudio cloud

python – Different behavior in the same conda-pytorch env on different GPUs

Want to improve this question? Add details and clarify the problem by editing this post. I have a project that uses conda env with old pytorch version. It works smoothly if I use Nvidia V100, but it won’t run on other GPUs (I’ve tried RTX3080, TeslaA10, RTX2080TI, TeslaA2, TeslaT4) using…

Continue Reading python – Different behavior in the same conda-pytorch env on different GPUs

Help Running LAMMPS Input Script in C++ on Windows – LAMMPS Development

I hope you’re doing well. I’m currently working on a project that involves running a LAMMPS input script from within a C++ program on Windows. I’ve been trying to figure it out on my own and have read through various resources, but I seem to have hit a dead end….

Continue Reading Help Running LAMMPS Input Script in C++ on Windows – LAMMPS Development

Bioconductor Code: SNPRelate

SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ==== ![GPLv3](http://www.gnu.org/graphics/gplv3-88×31.png) [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![R](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml/badge.svg)](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…

Continue Reading Bioconductor Code: SNPRelate

#1056648 – ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats

#1056648 – ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, r-pkg-team@alioth-lists.debian.net, wnpp@debian.org:Bug#1056648; Package wnpp. (Fri, 24 Nov 2023 11:00:03 GMT) (full text, mbox, link). Acknowledgement sent to Andreas Tille…

Continue Reading #1056648 – ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats

r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats

Package: wnpp Severity: wishlist Subject: ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats Package: wnpp Owner: Andreas Tille <ti…@debian.org> Severity: wishlist * Package name : r-cran-ggstats Version : 0.5.1 Upstream Author : Joseph Larmarange * URL : cran.r-project.org/package=ggstats * License : GPL-3+ Programming Lang: GNU R Description…

Continue Reading r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats

r-studio: “warning in install.packages: installation of package “spant” had non-zero exit status” problem

running R (version 4.2.2) and R Studio (version 1.4.1717), with 10GB of memory. trying to install the toolbox “spant” on HPC (high performance computer) cluster, and i get this error > Warning in install.packages: installation of package “spant” had non-zero exit status what am i missing to fix this? i…

Continue Reading r-studio: “warning in install.packages: installation of package “spant” had non-zero exit status” problem

normalize not left-normalizing?

I’m running plink2 to convert a vcf to a pgen with pseudobiallelic variants. Calling –normalize does not seem to left-normalize as I would expect, at least when I look at the .pvar. Log PLINK v2.00a6LM AVX2 Intel (21 Nov 2023)       www.cog-genomics.org/plink/2.0/(C) 2005-2023 Shaun Purcell, Christopher Chang  …

Continue Reading normalize not left-normalizing?

Rstudio crashes just before producing a brms model – General

Hello, I am trying to run a brms model with 20000 iterations. After many hours of simulations, and just before being done, Rstudio crashes without any warning. The model compiles successfully with 1000 iterations and, sometimes, with 10000 iterations but several attempts to run the model with 20000 iterations or…

Continue Reading Rstudio crashes just before producing a brms model – General

Accepted r-cran-rsqlite 2.3.3-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Tue, 21 Nov 2023 21:04:55 +0100 Source: r-cran-rsqlite Architecture: source Version: 2.3.3-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-cran-rsqlite (2.3.3-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: b8701a7d846703ed341b6d9f0da1772ede7b0025 2403 r-cran-rsqlite_2.3.3-1.dsc ce7d7f21085580a6ea1bd9790f621aecd23c170b…

Continue Reading Accepted r-cran-rsqlite 2.3.3-1 (source) into unstable

140releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.1.0 in configure

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/140releng-armv7-default/d5268d5f7157/logs/py39-pytorch-2.1.0.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=140releng-armv7-default&build=d5268d5f7157 Log: =>> Building misc/py-pytorch build started at Sun Nov 19…

Continue Reading 140releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.1.0 in configure

Nccl_external fails while trying to compile pytroch from source – torch.compile

Hello, I’m trying to compile pytorch from source and encountering the following build error. $ CC=gcc-10 CXX=g++-10 python setup.py develop … [5995/6841] Linking CXX executable bin/HashStoreTest Warning: Unused direct dependencies: /home/netfpga/research/collective/pytorch/build/lib/libc10.so /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_intel_lp64.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_gnu_thread.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_core.so.1 /lib/x86_64-linux-gnu/libdl.so.2 /home/netfpga/anaconda3/envs/pytorch_base/lib/libgomp.so.1 [5996/6841] Performing build step for ‘nccl_external’ FAILED: nccl_external-prefix/src/nccl_external-stamp/nccl_external-build nccl/lib/libnccl_static.a /home/netfpga/research/collective/pytorch/build/nccl_external-prefix/src/nccl_external-stamp/nccl_external-build /home/netfpga/research/collective/pytorch/build/nccl/lib/libnccl_static.a cd /home/netfpga/research/collective/pytorch/third_party/nccl/nccl &&…

Continue Reading Nccl_external fails while trying to compile pytroch from source – torch.compile

Installation of DESeq2 package while utilizing free Posit cloud – General

Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager)Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)BiocManager::install(“DESeq2”)‘getOption(“repos”)’ replaces Bioconductor standard repositories,…

Continue Reading Installation of DESeq2 package while utilizing free Posit cloud – General

DESeq2 installation failures

DESeq2 installation failures 0 Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager) Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2…

Continue Reading DESeq2 installation failures

Segmentation fault when running an NPT – User discussions

GROMACS version: 2023.2GROMACS modification: Yes/No Hello and good day, I am running some cycles of NVT-NPT for swelling procedures on a membrane. Each cycle goes like this NVT for 250 ps with T goes from 300-600 CNVT for 500 ps with T at 600 CNVT for 250 ps with T…

Continue Reading Segmentation fault when running an NPT – User discussions

DESeq2 design with unbalance data and a multifactor design

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

Continue Reading DESeq2 design with unbalance data and a multifactor design

DESeq2 with unbalanced dataset and multifactor design

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

Continue Reading DESeq2 with unbalanced dataset and multifactor design

Perl version error

[root@software ~]# perl -MFile::Copy -e ‘print $File::Copy::VERSION’ 2.39 [root@software ~]# perl -v This is perl 5, version 36, subversion 1 (v5.36.1) built for x86_64-linux Copyright 1987-2023, Larry Wall Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found…

Continue Reading Perl version error

Plink2 PCA approx memory allocation

This is great, thank you! Will this information be included in the PLINK2 documentation? The successful run we had included the log below. In the “Projecting random vectors” line, 21 steps are described, rather than the number 20 of requested principal components. I assume this is part of how the…

Continue Reading Plink2 PCA approx memory allocation

python – Docker with Rstudio & conda virtual env – unable to load R packages

I have this dockerfile: # Use the rocker/rstudio image with R version 4.1.2 FROM rocker/rstudio:4.1.2 # Install deps RUN apt-get update && apt-get install -y \ wget \ bzip2 \ bash-completion \ libxml2-dev \ zlib1g-dev \ libxtst6 \ libxt6 \ libhdf5-dev \ libcurl4-openssl-dev \ libssl-dev \ libfontconfig1-dev \ libcairo2-dev \…

Continue Reading python – Docker with Rstudio & conda virtual env – unable to load R packages

Improve setting up docs – ExecuTorch

escorciav (Victor Escorcia) November 9, 2023, 3:56pm 1 Hi all, Thanks a lot for putting out a quite detailed & easy to navigate documentation & tutorial! Now, Does anyone else feels that the docs jump from 0 to 1?What about linking concepts from How-it-works & High-level-overview into the setting things…

Continue Reading Improve setting up docs – ExecuTorch

[PATCH] gnu: Add python-scikit-learn-extra

From 59c388e64c12e39f7fb91ca538be332a130a3872 Mon Sep 17 00:00:00 2001 Message-ID: <59c388e64c12e39f7fb91ca538be332a130a3872.1699637173.git.timothee.mathieu@inria.fr> * gnu/packages/machine-learning.scm (python-scikit-learn-extra): New variable. Change-Id: I50992ceaa76608f3345df6d74a5d9e4aa7c485a5 — gnu/packages/machine-learning.scm | 41 +++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) Toggle diff (56 lines) diff –git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index a84377e1eb..1d0b796c68 100644 — a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1532,6 +1532,47 @@ (define-public python-scikit-learn data analysis.”) (license…

Continue Reading [PATCH] gnu: Add python-scikit-learn-extra

compilation error WRF | WRF & MPAS-A Support Forum

V4.3.3 No git found or not a git repository, git commit version not available. Compiling: WRF_EM_CORE Linux bcm1 5.14.0-162.22.2.el9_1.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Mar 30 17:01:52 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux GNU Fortran (GCC) 11.2.0Copyright (C) 2021 Free Software Foundation, Inc.This is free software; see the source for copying…

Continue Reading compilation error WRF | WRF & MPAS-A Support Forum

PLINK 1.9 meta-analysis

I’m trying to meta-analyze together some PLINK2 (“–glm omit-ref hide-covar cols=+a1freq,+beta”) outputs. I think I’m having trouble understanding the syntax requirement for the PLINK 1.9’s –meta-analysis feature.  I interpreted the doc as indicating that adding ‘logscale’ after the filenames would cause it to look for ‘BETA’ in the input.   PLINK…

Continue Reading PLINK 1.9 meta-analysis

Handle repository with different VCS folders.

Reported by Simon Tournier <zimon.toutoune@gmail.com> * guix/hash.scm (vcs-file?): Add optional argument for passing VCS kind of the file/repository. (file-hash*): Adjust accordingly. * guix/scripts/hash.scm (guix-hash)[file-hash]: Detect VCS kind of the file/repository and passes it. Change-Id: I8e286c3426ddefd664dc3a471d5a09e309824faa — guix/hash.scm | 18 ++++++++++++—— guix/scripts/hash.scm | 18 +++++++++++++—– 2 files changed, 25 insertions(+), 11…

Continue Reading Handle repository with different VCS folders.

plink1.9 chr23 extraction error

Just a quick update – I used PLINK2.0 which allowed me to pass through the public1.bim file but now there is a problem with the public.fam file. (C) 2005-2023 Shaun Purcell, Christopher Chang   GNU General Public License v3Logging to public1_filtered.log.Options in effect:   –bfile public1  –extract snp_ids_only.txt  –make-bed  –out…

Continue Reading plink1.9 chr23 extraction error

‘PC1’ entry on line 8297 of is categorical

> str(pheno_cov$PC1) num [1:10691] -0.0016 -0.001615 -0.001843 -0.001882 -0.000693 … PLINK v2.00a3.6LM AVX2 Intel (14 Aug 2022)     www.cog-genomics.org/plink/2.0/(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3Logging to ./res/test_plink2.log.Options in effect:  –bfile updateID_geno0.02_maf0.005  –ci 0.95  –covar ./pheno_cov/pheno_cov.txt  –covar-name Sex_Code,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10  –covar-variance-standardize  –glm hide-covar omit-ref  –memory 200000  –out…

Continue Reading ‘PC1’ entry on line 8297 of is categorical

Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb.

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable. Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b — gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) Toggle diff (51 lines) diff –git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79236ea26..ac09a079b4 100644 — a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -68,6 +68,42 @@ (define-module (gnu packages bioconductor) ;;; Annotations +(define-public r-bsgenome-hsapiens-ucsc-hg38-masked + (package + (name “r-bsgenome-hsapiens-ucsc-hg38-masked”) +…

Continue Reading Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb.

Plink2 –extract not working

Hi Chris,         This problem seems so silly but I just got stuck here for a long time.         I tried to extract a set of SNPs (I’m pretty sure they all appear in the .bim file) and rename their IDs with –set-all-var-ids, and…

Continue Reading Plink2 –extract not working

Plink Error

Plink Error 1 Hi I am trying to convert ped file for hapmap3 I downloaded here ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_format/ and unzipped with binzip2 but I am getting the following error when running this command PLINK v1.90b5.2 64-bit (9 Jan 2018) www.cog-genomics.org/plink/1.9/ (C) 2005-2018 Shaun Purcell, Christopher Chang GNU General Public License v3…

Continue Reading Plink Error

140releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure

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/140releng-armv7-default/08943441f26e/logs/py39-pytorch-2.0.1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=140releng-armv7-default&build=08943441f26e Log: =>> Building misc/py-pytorch build started at Thu Nov 2…

Continue Reading 140releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure

No valid entries in –score file

PLINK Error: No valid entries in –score file 0 Hi, I ran this command on plink1.9 to calculate the poligenic score. plink –vcf sample –score output.txt 1 2 3 –out poligenic_results – output.txt: ID ALT UKB-b-15541 rs10399793 C 0.000345793 rs2462492 T -0.00027716 – sample.vcf: #CHROM POS ID REF ALT QUAL…

Continue Reading No valid entries in –score file

Failed to download IlluminaHumanMethylationEPICv2anno.20a1.hg38

Failed to download IlluminaHumanMethylationEPICv2anno.20a1.hg38 1 I am currently working on illumina EPIC v1 and v2 data. When trying to annotate the v2 data I am unable to download the annotation package (note: the manifest package works fine). I get the error that the download failed and that ‘rhdf5filters’ is old….

Continue Reading Failed to download IlluminaHumanMethylationEPICv2anno.20a1.hg38

Add r-radiogx, r-coregx, r-piano, r-bench, r-profmem, r-relations, r-magicaxis, r-celestial, r-nistunits, r-r4rna and r-r3cseq.

* gnu/packages/bioconductor.scm (r-radiogx): New variable. Change-Id: I8fd06a18bd68f9a3baa2cc129d62aef06528bc97 — gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) Toggle diff (57 lines) diff –git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 091cf98b5c..69adea13e5 100644 — a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7848,6 +7848,50 @@ (define-public r-r4rna with numerical methods for computing statistics for each.”) (license license:gpl3))) +(define-public r-radiogx…

Continue Reading Add r-radiogx, r-coregx, r-piano, r-bench, r-profmem, r-relations, r-magicaxis, r-celestial, r-nistunits, r-r4rna and r-r3cseq.

[slurm-users] multiple srun commands in the same SLURM script

Here is my SLURM script: #!/bin/bash #SBATCH –job-name=”gpu_test” #SBATCH –output=gpu_test_%j.log # Standard output and error log #SBATCH –account=berceanu_a+ #SBATCH –partition=gpu #SBATCH –cpus-per-task=1 #SBATCH –mem-per-cpu=31200m # Reserve 32 GB of RAM per core #SBATCH –time=12:00:00 # Max allowed job runtime #SBATCH –gres=gpu:16 # Allocate four GPUs export SLURM_EXACT=1 srun –mpi=pmi2 -n 1 –gpus-per-node 1 python gpu_test.py & srun…

Continue Reading [slurm-users] multiple srun commands in the same SLURM script

epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience

Abstract Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5–8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new…

Continue Reading epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience

How to install or uninstall “r-bioc-genomeinfodb” on Linux Mint 21 “Vanessa” ?

1. Install r-bioc-genomeinfodb package In this section, we are going to explain the necessary steps to install r-bioc-genomeinfodb package: sudo apt install r-bioc-genomeinfodb Copy 2. Uninstall / Remove r-bioc-genomeinfodb package Please follow the guidance below to uninstall r-bioc-genomeinfodb package: sudo apt remove r-bioc-genomeinfodb Copy sudo apt autoclean && sudo apt…

Continue Reading How to install or uninstall “r-bioc-genomeinfodb” on Linux Mint 21 “Vanessa” ?

How to install or uninstall “r-bioc-scrnaseq” on Linux Mint 21 “Vanessa” ?

1. Install r-bioc-scrnaseq package Please follow the step by step instructions below to install r-bioc-scrnaseq package: sudo apt install r-bioc-scrnaseq Copy 2. Uninstall / Remove r-bioc-scrnaseq package This guide let you learn how to uninstall r-bioc-scrnaseq package: sudo apt remove r-bioc-scrnaseq Copy sudo apt autoclean && sudo apt autoremove Copy…

Continue Reading How to install or uninstall “r-bioc-scrnaseq” on Linux Mint 21 “Vanessa” ?

How to install or uninstall “r-bioc-htsfilter” on Linux Mint 21 “Vanessa” ?

1. Install r-bioc-htsfilter package This tutorial shows how to install r-bioc-htsfilter package: sudo apt install r-bioc-htsfilter Copy 2. Uninstall / Remove r-bioc-htsfilter package Please follow the instructions below to uninstall r-bioc-htsfilter package: sudo apt remove r-bioc-htsfilter Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of r-bioc-htsfilter package…

Continue Reading How to install or uninstall “r-bioc-htsfilter” on Linux Mint 21 “Vanessa” ?

Index of /~psgendb/birchhomedir/R/x86_64-redhat-linux-gnu-library/3.4/BiocParallel/html

Name Last modified Size Description Parent Directory   –   00Index.html 2018-08-29 08:43 23K   BatchJobsParam-class..> 2018-08-29 08:43 8.4K   BiocParallel-package..> 2018-08-29 08:43 1.3K   BiocParallelParam-cl..> 2018-08-29 08:43 9.2K   DoparParam-class.html 2018-08-29 08:43 4.0K   MulticoreParam-class..> 2018-08-29 08:43 19K   R.css 2018-08-29 08:43 1.3K   SerialParam-class.html 2018-08-29 08:43 3.2K  …

Continue Reading Index of /~psgendb/birchhomedir/R/x86_64-redhat-linux-gnu-library/3.4/BiocParallel/html

How to install or uninstall “r-bioc-drimseq” on Linux Mint 21 “Vanessa” ?

1. Install r-bioc-drimseq package This guide let you learn how to install r-bioc-drimseq package: sudo apt install r-bioc-drimseq Copy 2. Uninstall / Remove r-bioc-drimseq package Please follow the guidance below to uninstall r-bioc-drimseq package: sudo apt remove r-bioc-drimseq Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of…

Continue Reading How to install or uninstall “r-bioc-drimseq” on Linux Mint 21 “Vanessa” ?

Error in Gviz (actually, rtracklayer)

Error in Gviz (actually, rtracklayer) | IdeogramTrack 0 @25075190 Last seen 7 minutes ago South Korea When I run this code (below) iTrack <- IdeogramTrack(genome = “hg19”, chromosome = “chr2”, name = “”) then I get the error Error: failed to load external entity “http://genome.ucsc.edu/FAQ/FAQreleases” Did someone else encounter this…

Continue Reading Error in Gviz (actually, rtracklayer)

SageMath Download – upstream/ratpoints

SageMath Download – upstream/ratpoints Current Directory: upstream/ratpoints = ratpoints = == Description == Michael Stoll’s program which searches for rational points on hyperelliptic curves. == SPKG Maintainers == * Robert Miller == Upstream Contact == * Author: Michael Stoll * Email: Michael.Stoll@uni-bayreuth.de * Website: www.mathe2.uni-bayreuth.de/stoll/ == Dependencies == * GMP/MPIR…

Continue Reading SageMath Download – upstream/ratpoints

Error with remove.otus – mothur bugs

I got the following output when I used remove.otus: Linux version Using ReadLine,Boost,HDF5,GSL Distributed under the GNU General Public License Type ‘help()’ for information on the commands that are available For questions and analysis support, please visit our forum at forum.mothur.org Type ‘quit()’ to exit program [NOTE]: Setting random seed…

Continue Reading Error with remove.otus – mothur bugs

No samples in .vcf file.

I am trying to convert my vcf file into a BED format file.  When I use this command: plink –vcf merge.bacteria.vcf.gz –make-bed –out merge.bacteria.vcf.bed  I get the following error stating:  PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License…

Continue Reading No samples in .vcf file.

Bug#1054792: lammps: FTBFS: dh_install: error: missing files, aborting

Source: lammps Version: 20220106.git7586adbb6a+ds1-2 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu…@debian.org Usertags: ftbfs-20231027 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[2]: Entering directory ‘/<<PKGBUILDDIR>>/debian/build’ > make[2]: Nothing to be done for ‘preinstall’. >…

Continue Reading Bug#1054792: lammps: FTBFS: dh_install: error: missing files, aborting

Gromacs 2023 installation issue, slower run with gmx_mpi on multiple nodes – User discussions

GROMACS version: 2023GROMACS modification: NoHere post your question I am trying to install Gromacs 2023 on an HPC and hoping to do it correctly to get highest performance possible. HPC has Dual Intel Xeon Gold Skylake 6154 (3.0 GHz, 18-core) processors and Dual NVIDIA Tesla V100 PCIe 16 GB Computational…

Continue Reading Gromacs 2023 installation issue, slower run with gmx_mpi on multiple nodes – User discussions

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…

Continue Reading r – Issues with rqa in nonlinearTseries version 0.2.12 in RStudio

Plink2 error

I downloaded data from 1000 genomes website. MacBook-Air-4:plink_mac mac$ ./plink –vcf ALL.chr1.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf –make-bed –out char1 PLINK v1.90p 64-bit (13 Feb 2023)            www.cog-genomics.org/plink/1.9/ (C) 2005-2023 Shaun Purcell, Christopher Chang   GNU General Public License v3 Logging to char1.log. Options in effect:   –make-bed   –out char1…

Continue Reading Plink2 error

Index of /~psgendb/birchhomedir/R/x86_64-redhat-linux-gnu-library/3.4/bit64/html

Name Last modified Size Description Parent Directory   –   00Index.html 2018-08-29 08:40 34K   R.css 2018-08-29 08:40 1.3K   as.character.integer..> 2018-08-29 08:40 2.5K   as.data.frame.intege..> 2018-08-29 08:40 1.9K   as.integer64.charact..> 2018-08-29 08:40 2.2K   benchmark64.data.html 2018-08-29 08:40 1.8K   benchmark64.html 2018-08-29 08:40 9.1K   bit64-package.html 2018-08-29 08:40 68K  …

Continue Reading Index of /~psgendb/birchhomedir/R/x86_64-redhat-linux-gnu-library/3.4/bit64/html

gnu parallel – How to get reliable results on SLURM for performance tests?

I want to benchmark two algorithms ALG1 and ALG2 against each other using SLURM. Both binaries ALG1.o and ALG2.o contain serial implementations of the algorithms. In now, that ALG1.o is always faster than ALG2.o. Since I have thousands of experiments I want to use our cluster to run them. Each…

Continue Reading gnu parallel – How to get reliable results on SLURM for performance tests?

main-powerpc64le-default][misc/pytorch] Failed for pytorch-1.13.1_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/foul2/data/main-powerpc64le-default/pbc0e38d0f08e_s0afcac3e37/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=pbc0e38d0f08e_s0afcac3e37 Log: =>> Building misc/pytorch build started at Tue Oct 24…

Continue Reading main-powerpc64le-default][misc/pytorch] Failed for pytorch-1.13.1_1 in build

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…

Continue Reading r – unable to install Tidyverse in RStudio / Chromebook

Question on samtools view with –fast option

Question on samtools view with –fast option 0 Hi I had a question on samtools view with –fast option. I was trying to find any relevant docs and/or blogs detailing its usage and how best to use it. I could not find any and I thought I will ask the…

Continue Reading Question on samtools view with –fast option

[slurm-users] problem with slurm configuration and pmix

Hi I clone the slurm repository from github (version 23.11), and tried to configure it as follows: configure –config-cache –prefix=/usr/slurm_vm_23.11 –sysconfdir=/etc/slurm_vm_23 –with-http-parser=/usr/ –with-yaml=/usr/ –with-jwt=/usr/ –with-mysql_config=/usr/bin –enable-debug –with-pmix=/usr/lib/x86_64-linux-gnu/pmix2 But I receive the following error message: configure: error: unable to locate pmix installation I checked the pmix installation location, and it exists. I…

Continue Reading [slurm-users] problem with slurm configuration and pmix

Troubleshooting multallelic variant merging issue

Hello, I want to recode the IIDs of imputed data .bgen files into two different filesets, and merge these (working on eye-level analyses with Regenie). As I’m only interested in dosages, I’ve converted these to .pgen using PLINK2 (ref-first as UK Biobank): plink2 –bgen data.bgen ref-first –sample data.sample –update-ids recoded_ids_a.txt –make-pgen…

Continue Reading Troubleshooting multallelic variant merging issue

Different Output from lammps cpu vs gpu

Why energy/pressure are slighly off, what is possible solution for making them equal. Any suggestion/comment? clear package gpu 1 neigh no binsize 5.0 newton off units metal boundary p p p atom_style atomic variable lp equal “2.86” lattice bcc ${lp} orient x 1 0 0 orient y 0 1 0…

Continue Reading Different Output from lammps cpu vs gpu

DSA 5529-1: slurm-wlm security update

Home News Linux DSA 5529-1: slurm-wlm security update This website can use cookies to improve the user experience This website can use cookies to improve the user experience and to provide certain services and functions to users. Cookies contain small amounts of information (such as login information and user preferences)…

Continue Reading DSA 5529-1: slurm-wlm security update

Installing ‘tidyverse’ package for R/RStudio – General Help

With help from this forum, I was able to get R and RStudio working on Zorin 16 Lite. I now need to install the ‘tidyverse’ package for R, but attempting the install gives this error: $ sudo R (R starts up) > install.packages(“tidyverse”) Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is…

Continue Reading Installing ‘tidyverse’ package for R/RStudio – General Help

Deploying text-generation-webui – Build debugging

Hello everybody, I would be really thankful if you help.I am trying to deploy GitHub – oobabooga/text-generation-webui: A Gradio web UI for Large Language Models. Supports transformers, GPTQ, AWQ, llama.cpp (GGUF), Llama models. .Unfortunately I always get email that free-builder crashed due to insufficient RAM and get this error =>…

Continue Reading Deploying text-generation-webui – Build debugging

Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb?

Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb? 1 I want to run diamond and also get taxon identifiers for each hit. Is the only way to do this by incorporating it during the makedb step? Is there any other option? The reason…

Continue Reading Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb?

Accepted r-cran-ggplot2 3.4.4+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Tue, 17 Oct 2023 11:03:27 +0200 Source: r-cran-ggplot2 Architecture: source Version: 3.4.4+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-cran-ggplot2 (3.4.4+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: f33e42590eb14147963877ec97f5d75635be2fa9 2717 r-cran-ggplot2_3.4.4+dfsg-1.dsc 6f204d2b2ca03f0a68fc86ebea2e7a578e17f9de…

Continue Reading Accepted r-cran-ggplot2 3.4.4+dfsg-1 (source) into unstable

Unable to install Kmergenie

Unable to install Kmergenie 3 Hello there, I’m trying to install KmerGenie following the README file. I downloaded the kmergeni-1.6892.tar.gz, unzipped it and did make under the folder, but it didn’t work. It shows like the following julibio@DESKTOP-OTF949V ~/curso-bio/kmergenie/kmergenie-1.7051/kmergenie-1.7051 $ make cd ntCard && ./configure && make checking for a…

Continue Reading Unable to install Kmergenie

Accepted r-bioc-genomicranges 1.52.1+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 13 Oct 2023 15:27:21 +0200 Source: r-bioc-genomicranges Architecture: source Version: 1.52.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-genomicranges (1.52.1+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 9cbe72f1032af692a0089646e395779f6b3268bc 2283 r-bioc-genomicranges_1.52.1+dfsg-1.dsc 23359da02fc2fdb93ad69ebb2b97f37f2f676b48…

Continue Reading Accepted r-bioc-genomicranges 1.52.1+dfsg-1 (source) into unstable

Accepted r-bioc-tcgabiolinks 2.28.4+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 12 Oct 2023 10:59:27 +0200 Source: r-bioc-tcgabiolinks Architecture: source Version: 2.28.4+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-tcgabiolinks (2.28.4+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 57218af05f8bbbb7f01df36ad3451abf038279c7 2553 r-bioc-tcgabiolinks_2.28.4+dfsg-1.dsc 456c110e8f7b41ac18beb4ff696d8f7e17721702…

Continue Reading Accepted r-bioc-tcgabiolinks 2.28.4+dfsg-1 (source) into unstable

Line 15522 of data/Pheno_KFs1.txt has fewer tokens than expected in GWAS analysis

I’m performing GWAS using UKB imputed genetic data below. However, I got the error as follows. plink2 –bfile data_TL –glm hide-covar –pheno data/Pheno_KFs1.txt –pheno-name LogBUN_mg_dl –covar data/Covariatesdata.txt –covar-name PC{1..10}, Age, Tuoi, Sex –extract TL_snplist_All.txt –out output/GWAS_BUN.cvrtPLINK v2.00a6LM 64-bit Intel (27 Sep 2023)     www.cog-genomics.org/plink/2.0/(C) 2005-2023 Shaun Purcell, Christopher Chang…

Continue Reading Line 15522 of data/Pheno_KFs1.txt has fewer tokens than expected in GWAS analysis

Is Guix full-source bootstrap a lie?

One of the biggest concern, in my humble opinion, about the current state of this awesome story is non-deterministic compilations. And especially at early stages, for example gash-boot. $ guix build -e ‘(@@ (gnu packages commencement) gash-boot)’ $ guix build -e ‘(@@ (gnu packages commencement) gash-boot)’ –check guix build: error:…

Continue Reading Is Guix full-source bootstrap a lie?

linux – Error code 140 in command running through Nextflow on SLURM

[Note: question heavily edited to correspond to the actual problem] I’m trying to debug a command that fails only in specific conditions. The failure is with an exitcode 140, but I have no other information. This command is cat in_file | tr “\t” “\n” > out_file, and it is part…

Continue Reading linux – Error code 140 in command running through Nextflow on SLURM

Accepted r-bioc-genomeinfodb 1.36.4+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Mon, 09 Oct 2023 10:13:01 +0200 Source: r-bioc-genomeinfodb Architecture: source Version: 1.36.4+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-genomeinfodb (1.36.4+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 1ea8b5613eb598a608b6e39c3de208384130bce5 2300 r-bioc-genomeinfodb_1.36.4+dfsg-1.dsc 84d74990697576d9fd9ee2bc57e136af45aaec44…

Continue Reading Accepted r-bioc-genomeinfodb 1.36.4+dfsg-1 (source) into unstable

drivers/extcon/extcon-gpio.c – linux-imx – Git at Google

/* * extcon_gpio.c – Single-state GPIO extcon driver based on extcon class * * Copyright (C) 2008 Google, Inc. * Author: Mike Lockwood <lockwood@android.com> * * Modified by MyungJoo Ham <myungjoo.ham@samsung.com> to support extcon * (originally switch class is supported) * * This software is licensed under the terms of…

Continue Reading drivers/extcon/extcon-gpio.c – linux-imx – Git at Google

DiffBind dba.count() crash/can’t finish problems

I am using Diffbind for an ATAC-Seq analysis. My peak caller is MACS2, and here is my sample sheet: I run Diffbind with the following codes, but it crashed every time on dba.count . it can finished Computing summits… Recentering peaks… Reads will be counted as Paired-end. But have this…

Continue Reading DiffBind dba.count() crash/can’t finish problems

Getting error when trying to use pytorch 1.12.1 with jetpack version 5.1.1 – Jetson AGX Orin

When I am using Cuda 11.4 with the PyTorch 1.12 model on jetpack 5.1.1, I am getting error …torch::Device device_ = torch::kCUDAif (device_.is_cuda()) {c10::cuda::getCurrentCUDAStream().synchronize();}This runs fine but,const auto inputs =torch::from_blob(working_img.data,{working_img.rows, working_img.cols, 3}, torch::kUInt8).to(device_, torch::kFloat).permute({2, 0, 1}).contiguous();throws error[ERROR] [1696585409.990943029]: Segmentation error: CUDA error: no kernel image is available for execution on…

Continue Reading Getting error when trying to use pytorch 1.12.1 with jetpack version 5.1.1 – Jetson AGX Orin

Help Compiling STAR

It seems like you are facing issues with compiling STAR on your Ubuntu 20.04 LTS system. The error message indicates that the ‘cc’ command (which is the C compiler) is not found. This typically happens when the build environment is not set up correctly. Let’s try to troubleshoot this step…

Continue Reading Help Compiling STAR