Tag: SRC

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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r – Cannot Install maftools into BiocManager due to RSQLite

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

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Problem while running NEB, neb style ‘each’ – LAMMPS General Discussion

Hello everyoneI am sorry if the question is so bacis, acutally I am facing problem while running NEB and using the file style ‘each’. The calculation don’t run with the error of ‘Illegal NEB command (src/REPLICA/neb.cpp:124)’.I have all replicas initial configurations present in the directory and here is the simplest…

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Gromacs: nbnxn_sci Struct Reference

#include <gromacs/nbnxm/pairlist.h> Description Grouped pair-list i-unit. Public Member Functions int  numJClusterGroups () const   Returns the number of j-cluster groups in this entry.   Public Attributes int  sci   i-super-cluster   int  shift   Shift vector index plus possible flags.   int  cjPackedBegin   Start index into cjPacked.   int …

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aports – Alpine packages build scripts

not compatible with python3.11 as it still uses long deprecated getargspec API 5 tests fail: > […] > File “/home/buildozer/aports/testing/livestreamer/src/livestreamer-1.12.2/src/livestreamer/stream/__init__.py”, line 4, in <module> > from .akamaihd import AkamaiHDStream > File “/home/buildozer/aports/testing/livestreamer/src/livestreamer-1.12.2/src/livestreamer/stream/akamaihd.py”, line 15, in <module> > from ..packages.flashmedia import FLV, FLVError > File “/home/buildozer/aports/testing/livestreamer/src/livestreamer-1.12.2/src/livestreamer/packages/flashmedia/__init__.py”, line 4, in <module> >…

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lazy loading failed, unable to load shared object rtracklayer.so

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

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No module named ‘upstream_ontologist.tests’ (and more)

Source: lintian-brush Version: 0.134 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of lintian-brush the autopkgtest of lintian-brush fails in testing when that autopkgtest is run with the binary packages of lintian-brush from unstable. It passes when run with only packages from testing. In tabular form:…

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python – having problem with multi-gpu in pytorch transformer

I am currently trying to make a translation model with Trnasformer model through PyTorch. Since I have 2 GPUs (2080ti x 2) available for training, I want to train the model through multi-gpu. Currently, the gpu is assigned to 0 and 1 respectively. The way I use multi-gpu is to…

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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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New Best Practices — Visual Studio Magazine

The Data Science Lab Binary Classification Using PyTorch, Part 1: New Best Practices Because machine learning with deep neural techniques has advanced quickly, our resident data scientist updates binary classification techniques and best practices based on experience over the past two years. By James McCaffrey 10/05/2022 A binary…

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Language Modeling with LSTMs in PyTorch | by Essam Wisam | Sep, 2022

“Learning how to protect their affections at the genre, an assertive case of its own,” said the model. In the last three stories we discussed a lot about RNNs and LSTMs from a theoretical perspective. In this story, we will bridge the gap to practice by implementing an English language…

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Cellosaurus cell line LoVo (CVCL_0399)

Publications PubMed=1260746Drewinko B., Romsdahl M.M., Yang L.Y., Ahearn M.J., Trujillo J.M.Establishment of a human carcinoembryonic antigen-producing colon adenocarcinoma cell line.Cancer Res. 36:467-475(1976) PubMed=7104989; DOI=10.1016/0165-4608(82)90076-0Chen T.-R., Hay R.J., Macy M.L.Karyotype consistency in human colorectal carcinoma cell lines established in vitro.Cancer Genet. Cytogenet. 6:93-117(1982) PubMed=3335022Alley M.C., Scudiero D.A., Monks A., Hursey M.L.,…

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Swagger: Specify Two Responses with the Same Response Code

1. Overview In this article, we’ll write an API specification that allows returning two different objects for the same response code. We’ll demonstrate how we can use that specification to generate Java code and the Swagger documentation. 2. Presentation of the Problem Let’s define two objects. A Car has an…

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CRISPRa screen identifies a role for c-KIT signaling in tamoxifen resistance, potentially through upregulation of ABC transporters

Abstract Resistance to endocrine therapy is a common problem in patients with estrogen receptor alpha (ERα) positive breast cancer. In this study, we took a non-biased genome-wide approach to identify novel mechanisms of endocrine resistance using a clustered regularly interspaced short palindromic repeats (CRISPR) activating (CRISPRa) screen. Results from the…

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InnoCare Releases 2022 Mid-Year Results and Business Highlights

BEIJING–(BUSINESS WIRE)–InnoCare Pharma (HKEX: 09969), a leading biopharmaceutical company focusing on cancer and autoimmune diseases, today announced 2022 mid-year results which ended on June 30, 2022. Dr. Jasmine Cui, Co-founder, Chairwoman and CEO of InnoCare said: “The announcement of 2022 mid-year results coincides with our seventh anniversary. In the challenging…

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a new and efficient development model, to achieve code and API separation, efficient development, development must see!!!

什么是openapi 3.0 OpenAPI 3.0.0 是 OpenAPI The first official version of the specification,因为它是由 SmartBear Software 捐赠给 OpenAPI Initiative,并在2015年从 Swagger 规范重命名为 OpenAPI 规范. 介绍: OpenAPI 规范(OAS),is to define a standard、programming language-independentRESTful API的规范.OpenAPI Specifications enable both humans and computers to“Do not contact with any program source code and documentation、Does not monitor network…

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I cannot install “microbiome”

Hi there, i cannot install package “microbiome” in R (ver 4.2.1), when i input the code, it seems OK, BiocManager::install(“microbiome”, force = TRUE) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) ‘microbiome’ trying URL…

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Interfering B cell receptor signaling via SHP-1/p-Lyn axis shows therapeutic potential in diffuse large B-cell lymphoma | Molecular Medicine

Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403(6769):503–11. CAS  PubMed  Article  Google Scholar  Camicia R, Winkler HC, Hassa PO. Novel drug targets for personalized precision medicine in relapsed/refractory diffuse large…

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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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[Buildroot] [git commit branch/2022.02.x] package/libmodsecurity: needs dynamic library with libcurl and mbedtls

[Buildroot] [git commit branch/2022.02.x] package/libmodsecurity: needs dynamic library with libcurl and mbedtls – Peter Korsgaard From: Peter Korsgaard <peter@korsgaard.com> To: buildroot@buildroot.org Subject: [Buildroot] [git commit branch/2022.02.x] package/libmodsecurity: needs dynamic library with libcurl and mbedtls Date: Tue, 19 Jul 2022 18:35:54 +0200 [thread overview] Message-ID: <20220719162323.01D1283DF5@busybox.osuosl.org> (raw) commit: git.buildroot.net/buildroot/commit/?id=2d021a7e7163d13b604d508602288e7190ab63dc branch: git.buildroot.net/buildroot/commit/?id=refs/heads/2022.02.x

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Precompile errors with `pkg> update` or `pkg> add` for some packages – General Usage

In the package manager I was getting some precompilation errors when trying to update Julia. So I have removed all the offending packages, which included Pluto and tried to add Pluto again with the following result: (@v1.7) pkg> precompile (@v1.7) pkg> add Pluto Resolving package versions… Updating `~/.julia/environments/v1.7/Project.toml` [c3e4b0f8] +…

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Alternatives and detailed information of Prsice

PRSice (pronounced ‘precise’) is a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS). PRSice can run at high-resolution to provide the best-fit PRS as well as provide results calculated at broad P-value thresholds, illustrating results corresponding to either, can thin SNPs according to…

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Rsubread featurecounts

Rsubread featurecounts 1 Hi there, I seem to be getting this error when reading in a BAM file which was generated by PBMM2 align on pacbio data. I have tried to google the error message but there are no results. I wonder if anyone has ideas on what the error…

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autopkgtest needs update for new version of python-decorator)

Hi, I’d like to point out to this serious bug. Steffen, would you mind koordinating (not doing alone) an upgrade of the qiime infrastructure to make sure everything will go smoothly? Kind regards Andreas. Am Thu, Jun 30, 2022 at 11:30:21AM +0200 schrieb Paul Gevers: > Source: qiime > Version:…

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Error when adding new residue to hdb (CHARMM36) – User discussions

dom June 26, 2022, 2:05am #1 GROMACS version:2022.2GROMACS modification: No I am adding a new protein residue to the CHARMM36 forcefield (July 2021). As per the instructions in the GROMACS manual (“Adding a Residue to a Force Field”), I modified residuetypes.dat, aminoacids.rtp, and aminoacids.hdb with the new residue entry. It…

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autopkgtest regression with openssl 3

I raised the issue to the upstream developer, and he is working on it: github.com/grke/burp/issues/904 He is very responsive and gentle. On Tue, 24 May 2022 20:53:39 +0200 Sebastian Ramacher <sramac…@debian.org> wrote: > Source: burp > Version: 2.4.0-3 > Severity: serious > Tags: sid bookworm > > burp’s autopkgtest fail…

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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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Gene Set – TNFSF10

Dataset MSigDB Cancer Gene Co-expression Modules Category transcriptomics Type co-expressed gene Description tumor necrosis factor (ligand) superfamily, member 10|The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein preferentially induces apoptosis in transformed and tumor cells, but does not…

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python 3.x – PySpark on Jupyterhub K8s || Unable to query data || Class org.apache.hadoop.fs.s3a.S3AFileSystem not found

Pyspark Version: 2.4.5 Hive Version: 1.2 Hadoop Version: 2.7 AWS-SDK Jar: 1.7.4 Hadoop-AWS: 2.7.3 When I am trying to show data I am getting Class org.apache.hadoop.fs.s3a.S3AFileSystem not found while I am passing all the information which all are required. I passed all three for this config fs.s3.aws.credentials.provider org.apache.hadoop.fs.s3a.BasicAWSCredentialsProvider com.amazonaws.auth.InstanceProfileCredentialsProvider com.amazonaws.auth.EnvironmentVariableCredentialsProvider…

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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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Creating nacl in water system – User discussions

GROMACS version: 2018.6GROMACS modification: No I am very new to using gromacs, so I would appreciate any input.I am trying to set up a system of NaCl (JC) in water(spce) . I was able to run the tutorial simulation of lysozome in water. But in this the topology file was…

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Recombinant Feline EGF Protein, HEK293 Cells, hFc Tag, 62010-U01H

EGF Protein, Feline, Recombinant (ECD, hFc Tag): 产品信息 纯度 > 90 % as determined by SDS-PAGE. 生物活性 Testing in progress 蛋白构建 A DNA sequence encoding the Feline EGF (NP_001009381.1) (Asn969-Arg1020) was expressed with the fused Fc region of human IgG1 at the N-terminus. 表达宿主 HEK293 Cells 分子量 The…

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Sweeps while using MPI and SLURM – W&B Support

Hello! I am attempting to perform a hyperparameter search on my project, which uses MPI under the hood to aggregate the results of multiple agents. I have 63 agents that run an episode, returning a total reward at the end. At the end, each worker node sends their results to…

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NCBI C++ ToolKit: src/objtools/data_loaders/genbank/incr_time.cpp Source File

Go to the documentation of this file. Go to the SVN repository for this file. 44  const string& driver_name, 47  m_InitTime = x_GetDoubleParam(conf, driver_name, params.m_Initial); 48  m_MaxTime = x_GetDoubleParam(conf, driver_name, params.m_Maximal); 49  m_Multiplier = x_GetDoubleParam(conf, driver_name, params.m_Multiplier); 50  m_Increment = x_GetDoubleParam(conf, driver_name, params.m_Increment); 55  const string& driver_name, 68  if (…

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nf-core presentation – HackMD

<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg&#8221; –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg&#8221; width=”60%”></img></a> # What is nf-core\? [Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class=”fa fa-twitter” aria-hidden=”true”></i>@gau](https://twitter.com/gau/) | [<i class=”fa fa-github” aria-hidden=”true”></i>@maxulysse](https://github.com/maxulysse/) [Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/) Sweden — ## Overview – 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/) – 🧬 [NGI](https://ngisweden.scilifelab.se/) – 🍬 [Nextflow](https://www.nextflow.io/) – 🧙 [nf-core](https://nf-co.re/) — ##…

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Mbedtls Application On Tcp

How to use mbedTLS library in Keil or IAR IDEs? I want to do an RSA encryption/decryption using my AT91SAM7S256 ARM MCU.After googling I found mbed TLS library. The IP networking interface includes TLSSockets which behave similarly to normal TCP sockets but automatically use Mbed TLS to set up a…

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python – How can I respond to a CLI prompt in Kaggle?

I’m using Kaggle to generate poetry samples with GPT-2. My notebook uses datasets from Gwern’s poetry generator and uses nshepperd’s GPT-2 model. This all works fine with my notebook when generating unconditional samples. !python src/generate_unconditional_samples.py –top_k 40 –nsamples 1 –temperature 0.9 –model_name=1.5b-model –length=300 However, I want to generate samples with…

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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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ZC2 RNAseq | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.6412442 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg)](https://doi.org/10.5281/zenodo.6412442) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg :target: doi.org/10.5281/zenodo.6412442 HTML <a href=”https://doi.org/10.5281/zenodo.6412442″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg Target URL doi.org/10.5281/zenodo.6412442 Read more here: Source link

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AxelRosendahlHuber/Genotoxin_assay: Archiving code and data: Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.6424654 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg)](https://doi.org/10.5281/zenodo.6424654) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg :target: doi.org/10.5281/zenodo.6424654 HTML <a href=”https://doi.org/10.5281/zenodo.6424654″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg Target URL doi.org/10.5281/zenodo.6424654 Read more here: Source link

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Enable MBEDTLS debugging Nordic provided security backend (for CoAP Secure via OpenThread on nRF5340) – Nordic Q&A – Nordic DevZone

Goal Hi guys, is there an option to enable MBEDTLS debugging as with the CONFIG_MBEDTLS_DEBUG_LEVEL=4 for the MBEDTLS_BUILTIN? I am trying to setup a DTLS client based in order to establish a CoAP Secure Session via Openthread to a Borderrouter and I am struggling in the handshake process. It would…

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Compute shader not working – trying to just make it work at all – OpenGL

HI So, I want to try the compute shader to calculate transfer functions on my 3D texture, and output a new 3D texture, but I cant get it to work at all… Nothing happens. Right now I am just trying to fill the whole new 3D texture (outVolumeTexture) with values…

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golang-github-albenik-go-serial: autopkgtest regression on ppc64el: undefined: unix.TCGETS2

Source: golang-github-albenik-go-serial Version: 2.5.0-1 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of golang-github-albenik-go-serial the autopkgtest of golang-github-albenik-go-serial fails in testing when that autopkgtest is run with the binary packages of golang-github-albenik-go-serial from unstable. It passes when run with only packages from testing. In tabular form:…

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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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Bug#1008068: src:ocrad: fails to migrate to testing for too long: autopkgtest regression

Source: ocrad Version: 0.27-2 Severity: serious Control: close -1 0.28-1 Tags: sid bookworm User: release.debian….@packages.debian.org Usertags: out-of-sync Control: block -1 by 1004508 Dear maintainer(s), The Release Team considers packages that are out-of-sync between testing and unstable for more than 60 days as having a Release Critical bug in testing [1]….

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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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#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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Pymc3 linker error – v3

Hi all,I have been using pymc3 for about a year. A few months ago I changed from an intel mac to an M1 mac. Suddenly, I can’t use pymc3 anymore. I keep getting the following error that I have no idea how to interpret: You can find the C code…

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Gromacs: src/gromacs/selection/selmethod.cpp File Reference

#include “gmxpre.h” #include “selmethod.h” #include <cctype> #include <cstdarg> #include “gromacs/utility/arraysize.h” #include “gromacs/utility/cstringutil.h” #include “gromacs/utility/exceptions.h” #include “gromacs/utility/stringutil.h” #include “selmethod-impl.h” #include “symrec.h” This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Implements functions in selmethod.h. Author Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com static void  report_error (FILE *fp, const char…

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Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis

Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS  PubMed  Google Scholar  Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…

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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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Index of /~psgendb/doc/local/pkg/staden_2002.0/src/g

Name Last modified Size Description Parent Directory   –   freetree.h 2002-10-23 08:48 2.4K   g-connect.h 2002-10-23 08:48 588   g-db.h 2002-10-23 08:48 941   g-defs.h 2002-10-23 08:48 629   g-error.h 2002-10-23 08:48 2.0K   g-filedefs.h 2002-10-23 08:48 1.1K   g-files.h 2002-10-23 08:48 921   g-io.h 2002-10-23 08:48 1.4K  …

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Xena TCGA TARGET TCGx RNAseq Data

Zenodo DOI Badge DOI 10.5281/zenodo.6323594 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg)](https://doi.org/10.5281/zenodo.6323594) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg :target: doi.org/10.5281/zenodo.6323594 HTML <a href=”https://doi.org/10.5281/zenodo.6323594″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg Target URL doi.org/10.5281/zenodo.6323594 Read more here: Source link

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spring boot – How to make a synchronous call with WebClient using Open API Code Generator

Spring in RestTemplate documentation has note: As of 5.0 the class org.springframework.web.client.RestTemplate is in maintenance mode, with only minor requests for changes and bugs to be accepted going forward. Please, consider using the org.springframework.web.reactive.client.WebClient which has a more modern API and supports sync, async, and streaming scenarios docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/client/RestTemplate.html When I…

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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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Package – ismezy-youi-cli

$ npm install -g ismezy-youi-cli $ youi-cli COMMAND running command… $ youi-cli (-v|–version|version) ismezy-youi-cli/0.0.7 win32-x64 node-v14.15.3 $ youi-cli –help [COMMAND] USAGE $ youi-cli COMMAND … youi-cli $ youi-cli gencode <model.yml> USAGE $ youi-cli $ youi-cli gencode <model.yml> ARGUMENTS MODELPATH model文件路径 EXAMPLE $ youi-cli gencode model.yml See code: src/commands/gencode.ts youi-cli help…

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Generate Server Code Using OpenAPI Generator

In this weblog, you’ll learn to generate server code utilizing the OpenAPI Generator based mostly on an OpenAPI specification. The code will likely be generated for a Spring Boot Application, however OpenAPI helps many different languages which can be utilized. 1. Introduction In November I attended JFall, the biggest sooner…

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NCS v1.8.0: OpenThread: nrf-config.h: No such file or directory – Nordic Q&A – Nordic DevZone

I have a project using NCS v1.8.0 where I enabled openthread. For some reason, when trying to build `mbedtls/library/ecjpake.c`, the make command uses `-DMBEDTLS_CONFIG_FILE=”nrf-config.h”` and fails on: > nrf-config.h: No such file or directory I’m not sure why it tries to use this file because `MBEDTLS_CFG_FILE` is set to `config-tls-generic.h`….

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Find Transposon Element insertions using long reads (nanopore), by alignment directly. (minimap2)

find_te_ins is designed to find Transposon Element (TE) insertions using long reads (nanopore), by alignment directly. (minimap2) Install $ git clone github.com/bakerwm/find_te_ins.git&#13; $ cd find_te_ins Change the following variables upon your condition: genome_fa and te_fa in line-10 and line-11; $ bash run_pipe.sh run_pipe.sh Prerequisite minimap2 – 2.17-r974-dirty, align long…

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AWS IoT Core Integration with NVIDIA DeepStream error in make command – #3 by AnamikaPaul – DeepStream SDK

Please provide complete information as applicable to your setup. • Hardware Platform (Jetson / GPU) Jetson nano• DeepStream Version 6.00• JetPack Version (valid for Jetson only)• TensorRT Version• NVIDIA GPU Driver Version (valid for GPU only)• Issue Type( questions, new requirements, bugs)• How to reproduce the issue ? (This is…

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[PATCH v1 5/9] drm/bridge: ti-sn65dsi86: Fetch bpc via drm_bridge_state

[PATCH v1 5/9] drm/bridge: ti-sn65dsi86: Fetch bpc via drm_bridge_state – Sam Ravnborg From: Sam Ravnborg <sam@ravnborg.org> To: dri-devel@lists.freedesktop.org, Douglas Anderson <dianders@chromium.org> Cc: Rob Clark <robdclark@chromium.org>, Philip Chen <philipchen@chromium.org>, Jitao Shi <jitao.shi@mediatek.com>, Thomas Zimmermann <tzimmermann@suse.de>, Jonas Karlman <jonas@kwiboo.se>, Robert Foss <robert.foss@linaro.org>, Neil Armstrong <narmstrong@baylibre.com>, Jernej Skrabec <jernej.skrabec@gmail.com>, Andrzej Hajda <a.hajda@samsung.com>, Laurent…

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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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Quip potential – LAMMPS Development

Hi,I am trying to run quip pair_style in lammps ( 9 Nov 21) to perform MD using my trained gap potential. I trained GAP potential for sodium data using distance_2b and soap as descriptors. But when I run the input file, I get the following warnings and no data are…

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ambmax00/cp2k – Giters

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW….

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Gromacs: src/gromacs/nbnxm/kernels_reference Directory Reference

Directory dependency graph for kernels_reference: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Files file   kernel_gpu_ref.cpp   file   kernel_gpu_ref.h   Declares GPU reference kernel.   file   kernel_ref.cpp   file   kernel_ref.h   Declares CPU reference kernels.   file   kernel_ref_includes.h…

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CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally: docker run -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir cibersortx/fractions –username <my_user_name> –token <my_token> –single_cell TRUE –refsample reference.txt –mixture rsem_mixture_TPM.tsv –fraction 0 –rmbatchSmode TRUE I get the following output to the terminal: >Running…

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log repeats until it times out)

Your message dated Sat, 22 Jan 2022 21:52:05 +0100 with message-id <f98ce279-5828-d2b5-8b7c-88287a3ab…@debian.org> and subject line Re: Bug#997845: bug 997845 has caused the Debian Bug report #997845, regarding growlight: autopkgtest regression: log repeats until it times out to be marked as done. This means that you claim that the problem has…

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Pair_write with eam/alloy – error – LAMMPS General Discussion

Dear LAMMPS Users, I encountered a problem while trying to use pair_write command with an eam/alloy potential. pair_style hybrid eam/alloy table spline 100000 zbl 1.0 4.0pair_coeff * * eam/alloy Be_Agrawal.eam.alloy Be NULLpair_coeff 1 2 table DBe.potential-table DFT_DBEpair_coeff 2 2 zbl 1.0 1.0pair_write 1 1 100 r 1.0 6.0 table.txt metal…

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Adding ions ‘gmx grompp’ creates error “Atomtype ca not found” for ligand generated with GAFF – User discussions

GROMACS version: 2018GROMACS modification: No Hello, I am trying to run 200ns on protein-ligand complex and then calculate MMPBSA for the last 100 ns generated frames. I had some problems with ligand parameterization with cgenff, hence I used gaff…I have: GAFF to generate parameters for the ligand acpype to convert…

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MySQL always no result – Discussion

So I’ve been trying to create a custom system (kinda lika a garage system, but different) for my server.As I got to the part where I display the player all vehicles he ownes I need to create a server callback where the script gets all vehicles from the database using…

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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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Cannot install Phyloseq and dada2

Hello all, I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it’s because I don’t have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can’t seem to update the dependencies (“fansi”…

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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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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R connection to sqlite – Stackify

SQLite is a file level database, hence to reference it requires a full directory path. No where do you specify the working directory or a full path in the file name. By default, R will use the current working directory contained in getwd(). If database is not contained in this…

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scikit-survival | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5831584 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg)](https://doi.org/10.5281/zenodo.5831584) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg :target: doi.org/10.5281/zenodo.5831584 HTML <a href=”https://doi.org/10.5281/zenodo.5831584″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg Target URL doi.org/10.5281/zenodo.5831584 Read more here: Source link

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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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intermine/intermine: InterMine 5.0.6 | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5827966 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg)](https://doi.org/10.5281/zenodo.5827966) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg :target: doi.org/10.5281/zenodo.5827966 HTML <a href=”https://doi.org/10.5281/zenodo.5827966″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg Target URL doi.org/10.5281/zenodo.5827966 Read more here: Source link

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make Pyspark working inside jupyterhub

You need to configure the pyspark kernel. On my server jupyter kernels are located at: /usr/local/share/jupyter/kernels/ You can create a new kernel by making a new directory: mkdir /usr/local/share/jupyter/kernels/pyspark Then create the kernel.json file – I paste my as a reference: { “display_name”: “pySpark (Spark 1.6.0)”, “language”: “python”, “argv”: […

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Processed: src:pktanon: fails to migrate to testing for too long: autopkgtest regression on armhf

Processing control commands: > close -1 2~git20160407.0.2bde4f2+dfsg-8 Bug #1003104 [src:pktanon] src:pktanon: fails to migrate to testing for too long: autopkgtest regression on armhf Marked as fixed in versions pktanon/2~git20160407.0.2bde4f2+dfsg-8. Bug #1003104 [src:pktanon] src:pktanon: fails to migrate to testing for too long: autopkgtest regression on armhf Marked Bug as done >…

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Index of /~psgendb/doc/pkg/last/src

Name Last modified Size Description Parent Directory   –   Alignment.cc 2021-04-13 03:43 16K   Alignment.hh 2021-04-13 03:43 7.0K   AlignmentPot.cc 2021-04-13 03:43 703   AlignmentPot.hh 2021-04-13 03:43 2.1K   AlignmentWrite.cc 2021-04-13 03:43 22K   Alphabet.cc 2021-04-13 03:43 3.6K   Alphabet.hh 2021-04-13 03:43 2.3K   Centroid.cc 2021-04-13 03:43 20K  …

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Lammps in wsl – LAMMPS Installation

after making ubuntu in windows and installing the prerequisite commands ( sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tool)I downloadedLAMMPS Patch Release 14 Dec 2021 From www.lammps.org/download.htmland after extracting, I put it on the desktop. Next I entered…

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r markdown – Cant get r code to run in kaggle notebook

So I’m competing in the NFL Big Data Bowl hosted by Kaggle and I’m having trouble uploading both r script and rmd into kaggle. I keep getting parse errors that I can’t seem to get around. I’ve even tried copy pasting code from other peoples code from similar notebooks but…

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Bug#1003017: dulwich: autopkgtest regression: src/debian/tests/testsuite3: 10: -m: not found

Source: dulwich Version: 0.20.26-1 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of dulwich the autopkgtest of dulwich fails in testing when that autopkgtest is run with the binary packages of dulwich from unstable. It passes when run with only packages from testing. In…

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Tensorflow realizes kaggle cat and dog recognition (network design step by step)

This article is tensorflow edition ,pytorch The version will be given in the next blog Friendship tips : Try GPU, Blogger CPU Run on one VGG16 It took 1.5h… Tensorflow Realization kaggle Cat and dog recognition Online disk download link :pan.baidu.com/s/1kqfkr2X7mMkuFXb6C3KgTgExtraction code :xzyh kaggle Download it on the official website…

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MOLECULE package – LAMMPS Installation

Dear LAMMPS users, I want to run a LAMMPS simulation using HPC that include the Linux version of LAMMPS (14 Dec 2021), but I face the below error just after running the simulation: ERROR: Unrecognized atom style ‘full’ is part of the MOLECULE package which is not enabled in this…

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[Buildroot] [PATCH 1/2] package/mbedtls3: new package

[Buildroot] [PATCH 1/2] package/mbedtls3: new package * [Buildroot] [PATCH 1/2] package/mbedtls3: new package @ 2021-12-28 15:33 Fabrice Fontaine 2021-12-28 15:33 ` [Buildroot] [PATCH 2/2] package/hiawatha: needs mbedtls3 Fabrice Fontaine 2021-12-28 15:49 ` [Buildroot] [PATCH 1/2] package/mbedtls3: new package Thomas Petazzoni 0 siblings, 2 replies; 5+ messages in thread From: Fabrice…

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SageMath Cells ans CSS – githubmate

In the embedded SageMath Cells (see for instance mathifold.org/en/applet_hyperbolic_tessellations.html), the editor is currently hidden {% if page.sage %} <script src=”https://sagecell.sagemath.org/static/embedded_sagecell.js”></script> <script>$(function () { // Make *any* div with class ‘compute’ a Sage cell sagecell.makeSagecell({inputLocation: ‘div.sage’, hide: [“editor”, “evalButton”, “permalink”], autoeval: 1}); }); </script> {% endif %} (github.com/mathifold/mathifold/blob/master/_includes/head.html). However, it is…

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How do I “flush” data to my RSQLite disk database?

You’re not using the pattern suggested by the RSQLite documentation. That documentation uses dbWriteTable to copy a data frame into a SQLite table: dbWriteTable(con, “mtcars”, mtcars) According to this documentation, your full code would look something like this: con <- dbConnect(RSQLite::SQLite(), “./mtcars.db”) data(mtcars) dbWriteTable(con, “mtcars”, mtcars) dbListTables(con) # Fetch all…

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sqldf : create table from data frame error: “no such table”. and two tables created instead of one

UPDATE: newest versions of RSQLite and sqldf do not have the incompatibility issues addressed by this question i.e.: sqldf_0.4-10 RSQLite_1.1-2 work together well – Nathan All: Thanks to G. Grothendieck for pointers to incompatibility issues introduced by RSQLite 1.1-1. As stated in the comment to the answer, downgrade RSQLite to…

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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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kojix2/ruby-htslib: v0.0.4 | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5797825 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg)](https://doi.org/10.5281/zenodo.5797825) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg :target: doi.org/10.5281/zenodo.5797825 HTML <a href=”https://doi.org/10.5281/zenodo.5797825″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg Target URL doi.org/10.5281/zenodo.5797825 Read more here: Source link

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r – RSQLite Error “hash is not an exported object”

I am trying to scrape some pitchf/x data and store it in an SQLite database. However, I am receiving the following error when I run the following code: library(RSQLite) library(dplyr) db <- src_sqlite(“pitchfx.sqlite3”, create = T) This is the error: Error in h(simpleError(msg, call)) : error in evaluating the argument…

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Bioinformatics Engineer – Idealist

POSITION SUMMARY The Simons Foundation is seeking a Bioinformatics/Senior Bioinformatics Engineer (dependant upon experience) to develop and support whole exome and genome sequence data analysis pipelines in both research and operational modalities. This position will report to the Director of Data and Analytics in the informatics group and will work…

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bioinformatics – Local BLAST NCBI C++ Exception

I’m getting an error trying to to use blast v2.12 against a local nt database. I’ve downloaded nt twice from the ftp server thinking the first time it was corrupt but that didn’t change anything. My command is: blastn -db nt -num_threads 8 -outfmt “6 qseqid sacc stitle ssciname nident…

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Gromacs: src/gromacs/gmxpreprocess Directory Reference

Directory dependency graph for gmxpreprocess: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Directories directory   tests   Files file   add_par.c   file   add_par.h   file   calch.c   file   calch.h   file   convparm.c   file   convparm.h  …

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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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Bug#1001735: node-trust-keyto: autopkgtest regression: Cannot find module ‘@trust/keyto’

Source: node-trust-keyto Version: 2.0.0~alpha1-1 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of node-trust-keyto the autopkgtest of node-trust-keyto fails in testing when that autopkgtest is run with the binary packages of node-trust-keyto from unstable. It passes when run with only packages from testing. In…

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

Source: minimap2 Version: 2.17+dfsg-12 Severity: serious Control: close -1 2.22+dfsg-3 Tags: sid bookworm User: release.debian….@packages.debian.org Usertags: out-of-sync Dear maintainer(s), The Release Team considers packages that are out-of-sync between testing and unstable for more than 60 days as having a Release Critical bug in testing [1]. Your package src:minimap2 has been…

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