Tag: GNU

query regarding error in installation of “goseq” R bioconductor package

query regarding error in installation of “goseq” R bioconductor package 0 @6d5973d2 Last seen 19 hours ago India I am trying to install “goseq” Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are…

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ANGSD | FSU Research Computing Center

Introduction ANGSD is a software for analyzing next generation sequencing data intended for use with mapped reads to imputed genotype probabilities. ANGSD can work with BAM files but is not meant for manipulating them. SAMTools is best for that. ANGSD is ideal for use with low to medium depth genomic…

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r – monocle3 installation issues

I have R 4.2.1 and the latest R studio build 554 on a macOS Monterey. I am trying to install monocle3 using the following : BiocManager::install(‘monocle3’) I get a really long error message BiocManager::install(“monocle3”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15…

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Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS  PubMed  PubMed Central  Google Scholar  Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS  PubMed  PubMed Central  Google Scholar  Yokoyama, A….

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GPU inference doesn’t work when importing open3d

Thanks for your error report and we appreciate it a lot. Checklist I have searched related issues but cannot get the expected help. I have read the FAQ documentation but cannot get the expected help. The bug has not been fixed in the latest version. Describe the bug The GPU…

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r – View() function in RStudio Server opens new tab but does not display data

I am running an Ubuntu 18.04.6 LTS server on Google Cloud Compute Engine. I have downloaded RStudio Server onto my machine and kept getting this message: Warning message: R graphics engine version 15 is not supported by this version of RStudio. The Plots tab will be disabled until a newer…

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GROMACS Installation Problem in The Grid Computer – User discussions

GROMACS version: 2021.2GROMACS modification: No Hello all, I am new to GROMACS. I wanted to install it on a grid computer servers supported by the government and I’ve done step by step instructions in the following link (The language of the instructions is in Turkish but you may find the…

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Potential file is missing an entry – LAMMPS General Discussion

Dear all, I am using LAMMPS to simulate some thermodynamic properties of b-SiGe. I found the potential file in the official github repository for LAMMPS . The first part of my code is this ############################################################### #1 general units metal dimension 3 atom_style atomic neighbor 0.3 bin #2 structure boundary p…

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[slurm-users] “Plugin is corrupted” message when using drmaa / debugging libslurm

On 28/06/2022 23:14, Chris Samuel wrote: > On 28/6/22 12:19 pm, Jean-Christophe HAESSIG wrote: Hi, Yes I also found it and that’s where I saw the detailed debug3 & debug4 calls. > it’s when it’s checking it can load the plugin and not hit any > unresolved library symbols. The…

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Ubuntu Manpage: bamfillquery – fill query sequences into BAM files

Provided by: biobambam2_2.0.179+ds-1_amd64 NAME bamfillquery – fill query sequences into BAM files SYNOPSIS bamfillquery [options] <in.bam queries.fasta >out.bam DESCRIPTION bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data…

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Unexpected behaviour during hybrid Monte-Carlo simulations (ReaxFF) – LAMMPS Beginners

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)…

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ERROR No such moleculetype NA – User discussions

GROMACS version:GROMACS modification: Yes/No I got this errorwhen I run the line: gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 10in the topol.top there is 3 NA atoms 🙂 GROMACS – gmx grompp, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C….

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parallel downloads from SRA with SRA toolkit or other ways to speed up downloads

parallel downloads from SRA with SRA toolkit or other ways to speed up downloads 0 Is there a way to parallelize downloads from NCBI using SRAToolkit on a HPC cluster? I tried using GNU parallel but I can not actually tell if the downloads are doing anything: cat < /home/ptellier/scratch/phillip/data/escc_data/SRA_accessions.txt…

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Convert ONNX RuntimeError: tin_shift_forward_impl: implementation for device cpu not found.

when convert tin to onnx meet this issue: RuntimeError: tin_shift_forward_impl: implementation for device cpu not found. env:sys.platform: linuxPython: 3.8.10 (default, Jun 2 2021, 10:49:15) [GCC 9.4.0]CUDA available: TrueGPU 0,1: Tesla T4CUDA_HOME: /usr/local/cudaNVCC: Cuda compilation tools, release 11.4, V11.4.120GCC: x86_64-linux-gnu-gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0PyTorch: 1.9.1+cu111PyTorch compiling details: PyTorch built with: GCC 7.3…

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#1012224 – python-tornado: autopkgtest regression in testing

#1012224 – python-tornado: autopkgtest regression in testing – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, Debian Python Team <team+python@tracker.debian.org>:Bug#1012224; Package src:python-tornado. (Wed, 01 Jun 2022 18:00:03 GMT) (full text, mbox, link). Acknowledgement sent to Graham Inggs <ginggs@debian.org>:New Bug report received…

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fix checkpatch.pl struct should normally be const — DRI Development

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…

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Accepted r-bioc-rgsepd 1.28.0-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 17 May 2022 08:43:38 +0200 Source: r-bioc-rgsepd Architecture: source Version: 1.28.0-1 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 (1.28.0-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1:…

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Accepted r-bioc-scrnaseq 2.10.0+ds-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 17 May 2022 07:49:00 +0200 Source: r-bioc-scrnaseq Architecture: source Version: 2.10.0+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 (2.10.0+ds-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version:…

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Accepted r-bioc-rsubread 2.10.0-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 12 May 2022 14:00:29 +0200 Source: r-bioc-rsubread Architecture: source Version: 2.10.0-1 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-rsubread (2.10.0-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version:…

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Error while installing “object I is not exported by namespace:S4Vectors

met a problem while installing the LTLA/SingleR 1.5.3, urgent, thank you very much for help installing to /home/binf0xx/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-SingleR/00new/SingleR/libs ** R ** inst ** byte-compile and prepare package for lazy loading Error: object ‘I’ is not exported by ‘namespace:S4Vectors’ Execution halted ERROR: lazy loading failed for package ‘SingleR’ removing ‘/home/binf0xx/R/x86_64-pc-linux-gnu-library/4.0/SingleR’ Read…

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No rule to make target ‘/usr/lib/x86_64-linux-gnu/libpython3.10.so’

Source: opm-grid Version: 2021.10-3 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of opm-grid the autopkgtest of opm-grid fails in testing when that autopkgtest is run with the binary packages of opm-grid from unstable. It passes when run with only packages from testing. In tabular form:…

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Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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GDCquery_Maf error

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

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#1008368 – pigx-rnaseq: FTBFS: configure: error: R package rmarkdown not found.

#1008368 – pigx-rnaseq: FTBFS: configure: error: R package rmarkdown not found. – Debian Bug report logs Reported by: Lucas Nussbaum <lucas@debian.org> Date: Sat, 26 Mar 2022 21:12:04 UTC Severity: serious Tags: bookworm, ftbfs, sid Found in version pigx-rnaseq/0.0.19-2 Reply or subscribe to this bug. Toggle useless messages Report forwarded to…

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LAMMPS Patch Release 24 March 2022

LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…

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Accepted r-bioc-rsubread 2.8.2-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 21 Mar 2022 21:39:43 +0100 Source: r-bioc-rsubread Architecture: source Version: 2.8.2-1 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-rsubread (2.8.2-1) unstable; urgency=medium . * Team upload. * New upstream version * Maintainer:…

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Running rstudio (but not R alone) inside of a conda environment complains about finding Rccp.so

I find that when I try to load some packages in a conda environement, when using rstudio (but not when I’m using R directly), I get an error message about a missing Rcpp.so file. I activate my conda environment (which is running R version 4.1), open RStudio (which I installed…

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AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required

Hello, I am currently trying to install AnnotationHub but I am running into problems. I use R 4.0.4, renv (version 0.15.4) and BiocVersion 3.12. When I run BiocManager::install(“AnnotationHub”), I get the following error: Warning message: This project is configured to use R version ‘4.1.1’, but ‘4.0.4’ is currently being used….

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#1007974 – polyml: autopkgtest regression on amd64: relocation in read-only section `.text’

#1007974 – polyml: autopkgtest regression on amd64: relocation in read-only section `.text’ – 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#1007974; Package src:polyml. (Sat, 19 Mar 2022 20:39:04 GMT) (full text, mbox, link). Acknowledgement sent to Paul…

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Error on Rstudio cloud when installing DESeq2 package : rprogramming

Hi! I am using the free account on R studio cloud. And I am getting this error: * installing *source* package ‘DESeq2’ … ** using staged installation ** libs g++ -std=gnu++14 -I”/opt/R/4.1.2/lib/R/include” -DNDEBUG -I’/cloud/lib/x86_64-pc-linux-gnu-library/4.1/Rcpp/include’ -I’/cloud/lib/x86_64-pc-linux-gnu-library/4.1/RcppArmadillo/include’ -I/usr/local/include -fpic -g -O2 -c DESeq2.cpp -o DESeq2.o g++: fatal error: Killed signal terminated program…

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#1007732 – ccache: autopkgtest regression: cannot execute ‘cc1plus’

#1007732 – ccache: autopkgtest regression: cannot execute ‘cc1plus’ – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, Joel Rosdahl <joel@debian.org>:Bug#1007732; Package src:ccache. (Tue, 15 Mar 2022 20:27:05 GMT) (full text, mbox, link). Acknowledgement sent to Paul Gevers <elbrus@debian.org>:New Bug report received…

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Error installing package in RStudio – Software & Applications

Guys, I am trying to install this package on RStudio. I tried to install it on a windows virtual machine and it worked. I thought you guys could know what is happening and how to fix it. When I try to install the following happens: > install.packages(“minqa”) #This package is…

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Bioconductor – sccomp (development version)

DOI: 10.18129/B9.bioc.sccomp     This is the development version of sccomp; to use it, please install the devel version of Bioconductor. Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data Bioconductor version: Development (3.15) A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model…

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#1007013 – freecad: autopkgtest regression on arm64 and armhf: syntax error

#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…

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CHECK report for GGBase on malbec1

BioC 3.4: CHECK report for GGBase on malbec1 This page was generated on 2017-04-15 16:09:39 -0400 (Sat, 15 Apr 2017). GGBase 3.36.0VJ Carey Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) URL: hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GGBase Last Changed Rev: 122710 / Revision: 128728 Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) malbec1  Linux (Ubuntu 16.04.1 LTS) / x86_64   OK   OK  [ WARNINGS ] tokay1  Windows Server 2012 R2 Standard / x64   OK   OK   WARNINGS   OK  morelia  Mac OS X Mavericks (10.9.5) / x86_64   OK   OK   WARNINGS   OK  Summary Package: GGBase Version: 3.36.0…

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File “sage/symbolic/pynac_impl.pxi”, Exception. Unhandled SIGSEGV: A segmentation fault occurred

I am not sure if this is a bug in Python or sagemath. Using sagemath 9.5 on Linux Arch. I’ll describe the problem in words, then given MWE to reproduce it. I have an integrand integrand = “F(x)*(-x^2+x)^(1/2)” as string. I pass it to a subprocess using multiprocessing. When I…

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CP2K – Universitetet i Oslo

CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. Description CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional…

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No such file or directory)

I have R(version 4.1.2) installed on Fedora35. When I tried to install “DESeq2”, I got the following warning. 1: .inet_warning(msg) : installation of package ‘genefilter’ had non-zero exit status 2: .inet_warning(msg) : installation of package ‘locfit’ had non-zero exit status 3: .inet_warning(msg) : installation of package ‘DESeq2’ had non-zero exit…

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poem_openapi_derive – Rust

Docs.rs Releases Releases by Stars Recent Build Failures Build Failures by Stars Release Activity Rust The Book Standard Library API Reference Rust by Example Rust Cookbook Crates.io The Cargo Guide poem-openapi-derive-1.3.0 poem-openapi-derive 1.3.0 Docs.rs crate page MIT/Apache-2.0 Links Homepage Documentation Repository Crates.io Source Owners sunli829 Dependencies Inflector ^0.11.4 normal darling…

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Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

Control: reopen -1 Control: tags -1 confirmed Control: tags -1 upstream Control: forwarded -1 Christopher Chang <chrch…@alumni.caltech.edu> Hi Christopher (and Dylan), I verified the latest version (29 Jan 2022) of plink2 with the same result for the CI test we are doing in Debian (which was written by Dylan): $…

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bioconductor – Trouble installing Rhtslib in R/R studio

I’m using RStudio on Ubuntu 18 and I’m trying to install the htslib package from the Bioconductor repo, but I’m stuck now. This is what I get: * installing *source* package ‘Rhtslib’ … ** using non-staged installation via StagedInstall field ** libs cd “htslib-1.7” && make -f “/usr/lib/R/etc/Makeconf” -f “Makefile.Rhtslib”…

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Accepted r-bioc-tcgabiolinks 2.22.4+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sun, 30 Jan 2022 18:02:27 +0100 Source: r-bioc-tcgabiolinks Architecture: source Version: 2.22.4+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 (2.22.4+dfsg-1) unstable; urgency=medium . * New upstream version * dh-update-R to update Build-Depends…

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[lammps-users] installing lammps with cmake – LAMMPS Mailing List Mirror

Dear LAMMPS experts, I am trying to build lammps with cmake command with cmake3 by using this command line: cmake3 -C ../cmake/presets/most.cmake ../cmake It seemed that installation was successful according to the below report: — <<< Build configuration >>> Operating System: Linux CentOS Linux 7 Build type: RelWithDebInfo Install path:…

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How to fix deeptoolsintervals fatal error: python.h? ( Python, Python 3.X )

Problem : ( Scroll to solution ) I tried installing pip3 install deeptoolsintervals the error is: deeptoolsintervals/tree/tree.c:1:20: fatal error: Python.h: No such file or directory compilation terminated. error: command ‘/usr/bin/x86_64-linux-gnu-gcc’ failed with exit code 1 I have Ubuntu 16.04.7 and Python versions installed: ls /usr/bin | grep python dh_python2 dh_python3…

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Gst-nvivafilter – Jetson AGX Xavier

Platforms: Jetson AGX Xavier Jetpack 4.5 Cuda 10.2 IMX274 camera Hi fellow developers, I am having difficulties at making custom CUDA implementation. I have succesfully run the below pipeline. gst-launch-1.0 nvarguscamerasrc ! ‘video/x-raw(memory:NVMM), width=(int)3840, height=(int)2160, format=(string)NV12, framerate=(fraction)60/1’ ! nvivafilter cuda-process=true customer-lib-name=”libnvsample_cudaprocess.so” ! ‘video/x-raw(memory:NVMM), format=(string)NV12’ ! nvvidconv ! nvegltransform ! nveglglessink…

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Coul MSM – Segmentation Fault – LAMMPS Development

Without root access you cannot install gdb or valgrind from a package repository, but you can still install them by compiling from source. It is not too difficult, especially gdb. It just takes a little time. But the gdb information can make up for the time invested quickly. Please note…

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[slurm-users] Strange sbatch error with 21.08.2&5

Running test job with srun works: wayneh@login:~$ srun -G16 -p v100 /home/wayne.hendricks/job.sh 179851 Linux dgx1-1 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 179851 Linux dgx1-2 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Submitting the same with sbatch does…

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Fail to install Ensembl VEP

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

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traviz 1.0.0 installation fails: ERROR: lazy loading failed

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

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python – Where to upload the image files to JupyterHub server (ltjh)

I would like to create a jupyter notebook that displays some images like this. In the case of my computer, the image files are stored in the local device. So I wrote one-line tag to show the image. <img src=”images/python_with_Birds.gif” width=”400″/> But if I want to share my created jupyter…

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Running Jobs on Titan

Running Jobs on Titan Table of Contents Titan’s Job Scheduler – SLURM Documentation Translating to SLURM commands from other workload managers Basic SLURM Commands squeue sinfo scontrol sbatch scancel Titan’s Environment Module System – LMOD Listing all available modules on Titan Loading a module into your environment Listing all modules…

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How to build mbedtls for arm gcc

I want to use mbedtls for my stm32 projects, but I have some problems with building. I have to build mbedtls with arm-none-gcc compiler, right? My command is :(in build directory). CC=/home/jareeeeczek/Arczbit/Firmware/ProgramingRelated/ARM_GCC/gcc-arm-none-eabi-10-2020-q4-major/bin/arm-none-eabi-gcc CFLAGS=’-fstack-protector-strong’ cmake -DUSE_SHARED_MBEDTLS_LIBRARY=On ../ and I have error while compiling test program: none-eabi-10-2020-q4-major/bin/arm-none-eabi-gcc CFLAGS=’-fstack-protector-strong’ cmake – DUSE_SHARED_MBEDTLS_LIBRARY=On ../…

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[PATCH 0/3] Add Optuna.

* gnu/packages/machine-learning.scm (python-optuna): New variable. gnu/packages/machine-learning.scm | 96 +++++++++++++++++++++++++++++++ 1 file changed, 96 insertions(+) Toggle diff (116 lines) diff –git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index fd3e6b2090..3b6f709c4e 100644 — a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm #:use-module (gnu packages ocaml) #:use-module (gnu packages onc-rpc) #:use-module (gnu packages parallel) + #:use-module (gnu packages openstack) #:use-module (gnu packages perl)…

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Accepted r-cran-rsqlite 2.2.9-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Wed, 29 Dec 2021 01:12:39 +0530 Source: r-cran-rsqlite Architecture: source Version: 2.2.9-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Nilesh Patra <nil…@debian.org> Changes: r-cran-rsqlite (2.2.9-1) unstable; urgency=medium . * Team Upload. [ Andreas Tille ] * Disable…

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LAMMPS failed to install with Intel compiler due to cpio and diffutils

$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi (base) bash-4.2$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi [+] /opt/intel/cmake (external cmake-3.20.0-3teotjsa6webcsazofydfkk2v3pn2hb6) [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/alsa-lib-1.2.3.2-yctbppr2tcdayclbt32xjgagmmwbct2v [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/libiconv-1.16-ilxedtsoqggtmtbrjxehh6ojznmtdni3 [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/yasm-1.3.0-7y4fvxshqkmikii3cvelccaiajj4dboc [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/zlib-1.2.11-k24vg36ubsrvwfgrdipndmpqn4eo5jq7 ==>…

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A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Finding fuzzy seed matches enable BLEND to find both 1) exact-matching seeds…

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How to install package MbedTLS on julia-1.6.2?

I unzipped and copied to julia-1.6.2 to /opt/julia/ [root@srvr0 ~]# cp -a /root/Downloads/julia-1.6.2 /opt/julia/ Content of /etc/profile.d/julia.sh: export JULIA_HOME=/opt/julia/julia-1.6.2 export JULIA_LOAD_PATH=/opt/julia/julia-1.6.2/share/julia/stdlib/v1.6 export JULIA_DEPOT_PATH=/opt/julia/julia-1.6.2/share/julia/stdlib/v1.6 export JULIA_PKG_DEVDIR=/opt/julia/julia-1.6.2/share/julia/stdlib/v1.6 export JULIA_PROJECT=/opt/julia/julia-1.6.2/share/julia/stdlib/v1.6 export JULIA_HISTORY=/opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/logs/repl_history.jl Setting Environment Variables: [root@srvr0 ~]# source /etc/profile.d/julia.sh Invoking julia: [root@srvr0 ~]# julia _ _ _ _(_)_ | Documentation: docs.julialang.org (_) |…

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#1001716 – src:minimap2: fails to migrate to testing for too long: autopkgtest regression

#1001716 – src:minimap2: fails to migrate to testing for too long: autopkgtest regression – Debian Bug report logs Reported by: Paul Gevers <elbrus@debian.org> Date: Tue, 14 Dec 2021 20:03:02 UTC Severity: serious Tags: bookworm, sid Found in version minimap2/2.17+dfsg-12 Fixed in version minimap2/2.22+dfsg-3 Done: Paul Gevers <elbrus@debian.org> Reply or subscribe…

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Accepted r-bioc-drimseq 1.22.0-1 (source all) into unstable, unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 18 Nov 2021 21:20:39 +0100 Source: r-bioc-drimseq Binary: r-bioc-drimseq Architecture: source all Version: 1.22.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Steffen Moeller <moel…@debian.org> Description: r-bioc-drimseq – Differential transcript usage and tuQTL analyses with Changes: r-bioc-drimseq…

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RuntimeError: t == DeviceType::CUDAINTERNAL ASSERT FAILED when trying to calculate gradients

🐛 Describe the bug I am working on a constrained optimization problem using the augmented lagrange method. However, after calculating the first loss term in the optimization, I received the following error after trying to calculate the gradients with loss.backward(). /home/ihowell/Projects/validity/validity/generators/bern_vae.py:23: UserWarning: To copy construct from a tensor, it is…

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alphafold2: HHblits failed – githubmemory

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

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PyTorch model conversion – Technical Support

I’m unable to convert a model in pytorch This is the script to download the pretrained weights import torch import torchvision.models as models resnet18 = models.resnet18(pretrained=True) torch.save(resnet18, ‘resnet18.pt’) This is the script for converting ./convert –model-name resnet18 –platform pytorch –model resnet18.pt –input-size-list ‘3,224,224’ –mean-values ‘103.94,116.78,123.68,58.82’ –quantized-dtype asymmetric_affine –kboard VIM3 –print-level…

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Bioconductor URI, fallback and time-machine

Hi,On Tue, 03 Mar 2020 at 16:59, zimoun <zimon.toutoune@gmail.com> wrote: Toggle quote (17 lines) > Currently, the URI scheme (see ‘bioconductor-uri’ in> guix/build-system/r.scm) is:>> bioconductor.org/packages/release/data/<type-url-part>/src/contrib/<upstream-name>-<version&gt;.tar.gz>> which leads to 2 issues:>> 1. when Bioconductor updates their release, some package versions are> updated too, and so, the upstream return 404.> 2. for…

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Flavivirus-GLUE by giffordlabcvr

Overview The flaviviruses (family Flaviviridae) are a group of enveloped, positive-strand RNA viruses, many of which pose serious risks to human health on a global scale. Arthropod-borne flaviviruses such as Zika virus (ZIKV), Dengue virus (DENV), and yellow fever virus (YFV) are the causative agents of large-scale outbreaks that result…

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PhD Student Needed for Machine Learning (Deep Learning and Classical) in Molecular Biology

Job:PhD Student Needed for Machine Learning (Deep Learning and Classical) in Molecular Biology 0 Several openings are available immediately (or as late as Fall 2022) Looking for a highly motivated PhD student for Computational Biology research, with an algorithm development focus. The Ecological and Evolutionary Signal-processing (EESI) and Informatics lab…

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Ensembl vep singularity

Ensembl vep singularity 0 Hello all, I would like to use variant effect prédictor on an hpc cluster. For that i use singularity with the docker image of vep : singularity pull –name vep.sif But i have a problem to use one plugin because a perl module is missing….

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Question about ROH analysis by Plink 1.9

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

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R package error messages have missing package names

R package error messages have missing package names 0 Hi, I have R running with this sessionInfo -> R version 4.0.4 (2021-02-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 21.04 I am running into a problem with trying to install packages. Usually you get error messages that tell you which dependencies…

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Bioconductor – MotIV

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MotIV. Motif Identification and Validation Bioconductor version: 3.4 This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize…

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Accepted r-bioc-deseq2 1.32.0+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 14 Sep 2021 00:18:17 +0530 Source: r-bioc-deseq2 Architecture: source Version: 1.32.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Nilesh Patra <nil…@debian.org> Changes: r-bioc-deseq2 (1.32.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Team Upload. * New…

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Tau t gromacs manual

Tau t gromacs manual TAU at TACC – TACC User PortalBiomolecules | Free Full-Text | Electrostatics of Tau GN Drive Tau | The Gundam Wiki | Fandom Kirk took a break and sent out for coffee when a patrolman brought him…

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Finding the significance of the overlap between 2 or more gene sets using simulation in R.

TLDR: Example R function to calculate significance of overlap of 2 or more gene sets. genes_all is a vector that contains all genes, and gene_sets takes a list of vectors for each gene set. I encourage people to read the full tutorial and attempt to reproduce the code themselves (especially…

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gmod prop hunt not working

I’ve let the server stay open so you can join it and test for yourself. Game Garry’s Mod. It’s just textures (and maps, if you need it) for use as an addon to Garry’s Mod. From hunting down everyday objects in Prop Hunt to strangling and trampling pigs in Open…

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r-bioc-biocio — standard input and output for Bioconductor packages

Package: wnpp Severity: wishlist Subject: ITP: r-bioc-biocio — standard input and output for Bioconductor packages Package: wnpp Owner: Andreas Tille <ti…@debian.org> Severity: wishlist * Package name : r-bioc-biocio Version : 1.2.0 Upstream Author : Martin Morgan, * URL : bioconductor.org/packages/BiocIO/ * License : Artistic-2.0 Programming Lang: GNU R Description :…

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how to install packages in r

In classic R you will have to press the tab button to show the functions on the screen, although it should be noted that if the package contains many functions not all will be shown, as is the case with the ggplot2 package: Sometimes it can be interesting to inspect…

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Unicycler and GNU parallel

Unicycler and GNU parallel 1 Hi, unfortunately Unicycler forum is inactive and I would like to ask some info. I’m using a workstation of 56 CPUs with GNU parallel. When I’m running Unicycler with the “–threads 25” option is going “fast”. When I use GNU parallel, 2 jobs in parallel,…

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Blast locally on multiple fasta files with multiple database

Blast locally on multiple fasta files with multiple database 2 Hi all, I need to run blast locally on multiple fasta files contain in a directory. Previously, I have used command below: ls *.fasta | parallel -a – blastp -query {} -db my_database -evalue 0.00001 -qcov_hsp_perc 50 -outfmt 6 -max_target_seqs…

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Bioconductor – PICS

DOI: 10.18129/B9.bioc.PICS     Probabilistic inference of ChIP-seq Bioconductor version: Release (3.5) Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. Author: Xuekui Zhang <xzhang at stat.ubc.ca>, Raphael Gottardo <rgottard at fhcrc.org> Maintainer: Renan Sauteraud <rsautera at fhcrc.org> Citation (from within R, enter citation(“PICS”)): Installation To install this…

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PLINK Haplotype blocks estimation not working

Hi, I am using PLINK to estimate haplotype blocks using Gabriel’s method. I am using the following command plink –file Chr$PBS_ARRAY_INDEX –noweb –all –blocks –ld-window-kb 500 And it seemed to be working just fine but when job finished no blocks were called at all. The log file does not mention…

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install GenomicFeatures fail

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…

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Predicting and characterizing a cancer dependency map of tumors with deep learning

INTRODUCTION The development of novel cancer therapies requires knowledge of specific biological pathways to target individual tumors and eradicate cancer cells. Toward this goal, the landscape of genetic vulnerabilities of cancer, or the cancer dependency map, is being systematically profiled. Using RNA interference (RNAi) loss-of-function screens, Marcotte et al. (1),…

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GROMACS: src/gromacs/ewald/pme_pp.h | Fossies

GROMACS: src/gromacs/ewald/pme_pp.h | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/gromacs/ewald/pme_pp.h” (18 Aug 2021, 5141 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) C and C++ source code syntax highlighting (style: standard) with…

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GROMACS: src/gromacs/utility/any.h | Fossies

GROMACS: src/gromacs/utility/any.h | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/gromacs/utility/any.h” (18 Aug 2021, 8080 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) C and C++ source code syntax highlighting (style: standard) with…

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weird MAplot or volcano plot of DESeq2 diff result

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…

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Help speeding up HMMER’s HMMSearch algorithm for large fasta file with GNU Parallel

I’ve seen that HMMER can be sped up with GNU Parallel: Speed of hmmsearch I have around 100,000 sequences and a HMMER database of around 300 HMM profiles. I’m running everything at once but I’m wondering if it’ll be faster to split up the sequences and/or split up the jobs….

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Calculate LD matrix from bgen file

formatting error: Calculate LD matrix from bgen file 1 Hello, I am new to plink and am learning as I go. I am trying to calculate an LD matrix for a list of variants while using a bgen file as my reference population. See the command below: ./plink2/plink2 –r2 bin…

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