Tag: NAMESPACE

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

Hi,I’ve seen a few threads on RStudio terminal issues (e.g Cannot use terminal: no window contents – #4 by Aurele) but was not able to resolve on my system by toggling “connect with websockets” or changing between CMD Prompt, PowerShell, etc. The other options like “Local Terminal Echo” and “Save…

boost/type_traits/integral_constant.hpp // (C) Copyright John Maddock 2015. // Use, modification and distribution are subject to the // Boost Software License, Version 1.0. (See accompanying file // LICENSE_1_0.txt or copy at www.boost.org/LICENSE_1_0.txt) #ifndef BOOST_TYPE_TRAITS_INTEGRAL_CONSTANT_HPP #define BOOST_TYPE_TRAITS_INTEGRAL_CONSTANT_HPP #include <boost/config.hpp> #include <boost/detail/workaround.hpp> #if (BOOST_WORKAROUND(BOOST_MSVC, BOOST_TESTED_AT(1400)) \ || BOOST_WORKAROUND(BOOST_BORLANDC, BOOST_TESTED_AT(0x610)) \ || BOOST_WORKAROUND(__DMC__, BOOST_TESTED_AT(0x840))…

Hello community! This is my first post so I apologize if I am doing something wrong. I am running into an issue when trying to build pytorch-1.12.1 from source. I have search the web for a solution but cannot find one. I am not familiar with C++ so this stuff…

Mock implementation of an option storage class for unit testing. Provides facilities for checking that correct methods are called, and for controlling how they add values using the base class methods.   MockOptionStorage (const MockOption &settings)   Initializes the storage from option settings. More…   void  addDummyValue ()   Calls…

The Node.js team has recently released version 20.6.0, which brings improvements in environment variable configuration, module resolution, module customization, and experimental support for C++ garbage collection. In this patch, developers gain a new feature: built-in support for `.env` files. These files, following the INI file format, offer a simplified approach…

Hello, members. Does someone tell me how to how to specify a private image registry?(Usage of the singleuser.image.name configuration) 1. Environment Z2JH: 3.0.3 k8s: v1.27.4 OS: Ubuntu 22.04 2. Question Could you tell me how to specify a private image registry?(It it possible specify http instead of https?) Could you…

I have recently upgraded my Ubuntu version from 20.04 to 22.04 LTS and Rstudio-server to 2023.06.02. The R version is 4.3.1. After that the shiny App I am developing, which ran OK on the previous version, was giving an error of the type ‘libproj.so.15 – cannot open shared file’. After…

Hi, I’ve encountered a rather peculiar software issue involving the phyloseq package and the lme4 package when analyzing longitudinal microbiome data. Below, please find a reproducible example that triggers the error: First, when I run the mixed effects model code provided by lme4, it works perfectly: data(“sleepstudy”, package = “lme4”)…

boost/regex/v4/regex_token_iterator.hpp /* * * Copyright (c) 2003 * John Maddock * * Use, modification and distribution are subject to the * Boost Software License, Version 1.0. (See accompanying file * LICENSE_1_0.txt or copy at www.boost.org/LICENSE_1_0.txt) * */ /* * LOCATION: see www.boost.org for most recent version. * FILE regex_token_iterator.hpp *…

For some unknown reason, Rstudio is generating error messages while I m just typing (I’m not even pressing ENTER): Error in gsub(reStrip, “”, completions, perl = TRUE) : input string 1 is invalid UTF-8 Error in gsub(reStrip, “”, completions, perl = TRUE) : input string 1 is invalid UTF-8 Error…

I installed R a work administered computer (I don’t have admin rights). I also installed Rtools43. When I try to install packages from source, I am consistently getting the error described below. Details about system: > sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64…

This question already has answers here: Closed 18 hours ago. ] I tried to reinstall R studio the packages but i still have problem. I tried to install r tools as well to fix the issue. I tried another solutions as it can be seen. I…

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

Dear all, I downloaded new version of R studio , it is RStudio 2023.06.2-561 and I have an error : library( DESeq2)Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):namespace ‘rlang’ 1.0.6 is already loaded, but >= 1.1.0 is requiredLoading required package: DESeq2Error: package…

kghoon September 12, 2023, 6:29am 1 When adding the SameSite option to c.JupyterHub.tornado_settings, an error occurs while spawning a singleuser notebook. I am using the helm chart release version 3.0.3. The contents of the config.yaml file are as follows. hub: baseUrl: /jupyter config: Authenticator: admin_users: – root – “542380” JupyterHub:…

I’m running code in an R project after updating to newer versions of R/RStudio and the most recent tidyverse package versions. When I run certain dplyr/tidyverse functions, primarily joins, pivoting, or summarizing, I either have R crash, freeze, or get strange errors. For example, when I tried to summarize across…

I am aligning RNA-seq data to a custom reference using subjunc(): align.res <- subjunc(index=”Repvec”, file1=fwdname, readfile2=revname, output_file=bamname, nthreads = 6, sortReadsByCoordinates=TRUE) With the last parameter, the BAM file is sorted and the .bai file is created. Everthing is fine, when I load the BAM file into an genome viewer; however,…

I was trying to train a model in C++ API (libtorch) and got bad results. I then compared in a detailed way to pytorch. My network is very simple (linear with 4 inputs and outputs and only one hidden layer). In order to compare I set all in sequential in…

TCGAbiolinks not working anymore 0 The script in this tutorial does not work anymore bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html I get to GDCprepare stage and get error: Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix paper_ brca…

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

Hello, members 1. Questions Currently, there is the z2jh environment with singleuser.storage.type: dynamic.When I change the configuration to singleuser.storage.type: static,do I need to remove the current z2jh environment using helm delete jhub -n ns-z2jh?Or, Is it possible to change the configuration only?(Now I delete the z2jh environment. then re-create z2jh…

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

pytorch-2.1.0-rc3.tar.gz: …/csrc/onnx/init.h | Fossies “Fossies” – the Fresh Open Source Software Archive Member “pytorch-2.1.0-rc3/torch/csrc/onnx/init.h” (6 Sep 2023, 153 Bytes) of package /linux/misc/pytorch-2.1.0-rc3.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…

For several weeks now, every time I try to open R Studio I encounter a message telling me that “The R session failed to start” (see below). I’ve repeatedly deleted and reinstalled both R and R studio for Mac OS and have turned off all VPNs and Firewalls on my…

R Session Startup Failure Report RStudio Version RStudio 2023.06.2+561 “Mountain Hydrangea ” (de44a311, 2023-08-25) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.06.2+561 Chrome/110.0.5481.208 Electron/23.3.0 Safari/537.36 Error message [No error available] Process Output The R session exited with code 1. Error output: [No errors emitted]…

We have RHEL8 FIPS enabled OS linux machines ( Red Hat Enterprise Linux release 8.8 (Ootpa), 4.18.0-477.13.1.el8_8.x86_64 #1 SMP Thu May 18 10:27:05 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux ) and have a very simple java client running on that machine to connect to K8s client to list the pods….

I cleaned some of my files from my computer using CleanMyMacX software, and now when I try to open Rstudio, I get a fatal error message. It also says [No error available]. I tried downloading and redownloading R and RStudio and no luck. The regular R console seems to be…

Hello, Members. 1. Overview I’m a newbie about Z2JH (and k8s). I installed Z2JH with the following command. As a result, the hub node shows the status PENDING. kubectl describe show the following message. 0/4 nodes are available: pod has unbound immediate PersistentVolumeClaims. preemption: 0/4 nodes are available: 4 No…

The Saloon SDK generator package for Saloon will help you generate SDKs from Postman collections and OpenAPI specifications. This unlocks the potential to generate full clients that you can update quickly whenever your API spec changes. Imagine introducing a GitHub workflow in the API CI pipline that triggers an SDK…

When you think about making your microservice architecture more secure, would you know where to start? There are so many ways to begin securing a system that it quickly becomes overwhelming. This blog post introduces you to two approaches to minimize security exposure. It starts with documentation What does documentation…

Hi, R studio server freezes and the .Rproj.user and .Rhistory files must be deleted to connect to an already running session. This behaviour is only resolved by uninstalling monocle3 and comes back when I re-install monocle3. I tried the development and beta branch of Monocle3. I had the same issue…

I am currently using a shared server running CentosOS7. I am trying to run RStudio IDE off it and had some trouble installing sf and s2 because the version of GDAL was not up to date. However, that was fixed by loading GDAL 3.1.3. However, whenever I try to load…

I am trying to use DEXseq and I was told that I could output normalized counts using the following method by my supervisor: library(“DEXSeq”) # Create the DEXSeqDataSet object dxd <- DEXSeqDataSetFromHTSeq( countsFiles, sampleData=sampleTable, design= ~ sample + exon + condition:exon, flattenedfile=flattenedFile ) #Normalize normFactors <- matrix(runif(nrow(dxd)*ncol(dxd),0.5,1.5), ncol=ncol(dxd),nrow=nrow(dxd), dimnames=list(1:nrow(dxd),1:ncol(dxd))) normFactors…

enter image description here Hi I have been trying to import by data from an excel file into Rstudio. I usually just press the import dataset button in the environment pane. It lets me browse and select my file I want to import and then I get this error message…

PCA percent variance DESeq2 0 @6d1ed6fa Last seen 14 hours ago United States I saved ‘pcaData’ as a data frame for future use. I ran the following to get vector ‘percentVar’, however, it is empty. Do I need the data in a different format to extract percent variance? > pcaData…

Please can someone help me with the below error messages encountered while trying to install the “tidyverse” package and loading it. install.packages(“tidyverse”)WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding: cran.rstudio.com/bin/windows/Rtools/Installing package into ‘C:/Users/PC/AppData/Local/R/win-library/4.3’(as ‘lib’…

I have been attempting to install a package that requires cmake. However, Rstudio can’t seem to find it for some reason: R version 4.3.1 (2023-06-16) — “Beagle Scouts” Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin22.4.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY….

Hi all, I am following the ATACseq normalization and analysis pipeline outlined in this manuscript Reske et. al, 2020, and I am at the point of processing the MACS2 output in R. I used the following commands to specify my bamfiles, set the discard parameter to the blacklist for mm10,…

I have included cds-swagger-ui-express within my application to auto-generate the openAPI documentation as well as host it from the server itself. I was looking for a way to auto-generate the error response documentation by swagger itself. Below is my code with the existing document that is generated // srv/todo-service.js const…

We can fine-tune the Torchvision pretrained semantic segmentation models on our own dataset. This has the added benefit of using pretrained weights which leads to faster convergence. As such, we can use these models for multi-class semantic segmentation training which otherwise can be too difficult to solve. In this article,…

Hi all, I try to filter out gene with low count from raw count matrix I run d <- DGEList(counts=counts,group=factor(conditions)) keep <- filterByExpr(d) bcv <- 0.2 et <- exactTest(keep, dispersion=bcv^2) Error in exactTest(d, dispersion = bcv2) : Currently only supports DGEList objects as the object argument. d <- estimateTagwiseDisp(d) Error…

Introduction to Deep Learning – Part 5 Introduction to Deep Learning – Part 5 In Introduction to Deep Learning – Part 4 of this series, we started to get our hands dirty in using PyTorch, a popular open source deep learning framework called PyTorch. In this article, we will continue…

Image Created by Author with Playground AI   Before we dive into the details of this exciting development, let’s explore a scenario to understand it better. Picture yourself as a Senior Data Scientist leading a sophisticated image classification project. Your TensorFlow-based model is performing remarkably well. However, as you add…

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

I was directed here via this issue on github. I assume this is not a bug and is instead a support request as tagged. The issue is 3175 in jupyterhub/zero-to-jupyterhub-k8s, but unfortunately I’m limited to 2 links per post as as new user. I am running z2jh via EKS on…

Description What steps will reproduce the problem? I have created a virtual environment and installed PyTorch library there. When I execute the statements import torch x = torch.rand(3) the code works, and output is displayed but this internal error keeps popping up. I don’t know what’s the issue. Traceback Exception…

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/beefy2/data/124amd64-quarterly/1c331580481c/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/beefy2/build.html?mastername=124amd64-quarterly&build=1c331580481c Log: =>> Building misc/pytorch build started at Thu Jul 27…

Google Cloud and SAP have been partners for many years, helping customers like Southwire transform their businesses by migrating their SAP environments to Google Cloud, and leveraging services like Vertex AI, Document AI and BigQuery, so they can get insights faster and accelerate business transformation.  SAP developers and architects have…

Hello, I would like your suggestions for this error with rma() function, for analysing microRNA-affymetrix data. I downloaded the package cdf (miRNA-4_0-st-v1_CDF) (provided below), created the package with make.cdf.package, installed it with R CMD INSTALL. library(makecdfenv) make.cdf.package(filename = “miRNA-4_0-st-v1.cdf”, packagename = “miRNA-4_0-st-v1.cdf”, cdf.path = “./miRNA_4_0_CDF/”, package.path= “/shared/home/mkondili/Tools_Packages/”, compress = FALSE,…

Symfony bundle for easy JSON-RPC server OpenAPI 3.0.0 documentation Symfony bundle for yoanm/jsonrpc-http-server-openapi-doc-sdk Versions Symfony v3/4 – PHP >=7.1 : ^v0.X Symfony v4/5 – PHP >=7.2 : ^v1.0 How to use Once configured, your project is ready to handle HTTP GET request on /doc/openapi.json endpoint. Result will be a openapi…

R Session Startup Failure Report RStudio Version RStudio 2023.06.1+524 “Mountain Hydrangea ” (547dcf86, 2023-07-07) for windows Description of issue –RStudio does not start and reports ” Error Starting R – The R session failed to start.” Attempted steps taken to fix –I removed the previous version of R, and also…

Collaboration diagram for Help Formatting for Online Help (onlinehelp): This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Description Provides functionality for formatting help text for console and reStructuredText. This module provides helper functions and classes for formatting text to the console and as…

…[4742/6394] Generating …/…/…/include/sleef.hGenerating sleef.h: mkrename cinz_ 2 4 __m128d __m128 __m128i _m128i SSE2Generating sleef.h: mkrename cinz 2 4 __m128d __m128 __m128i _m128i SSE2 sse2Generating sleef.h: mkrename cinz 2 4 __m128d __m128 __m128i _m128i SSE2 sse4Generating sleef.h: mkrename cinz 4 8 __m256d __m256 __m128i struct\ {\ _m128i\ x,\ y;\ } AVXGenerating…

Dear all, This is my first post so lets hope write it well.I’m trying to make a connection through ODBC by System DSN.I don´t know why I obtain “No tables”. Blockquote Session info: sessionInfo()R version 4.3.1 (2023-06-16 ucrt)Platform: x86_64-w64-mingw32/x64 (64-bit)Running under: Windows 10 x64 (build 19044) Matrix products: default locale:[1]…

image: How refget works view more  Credit: Stephanie Li / GA4GH   A widely-used tool that finds the exact references needed to pinpoint differences in our DNA just got a refresh. On 17 July, the Standards Steering Committee of the Global Alliance for Genomics and Health (GA4GH) voted to release refget v2.0….

I am fairly new to ggtree and it had been working until today. Today, several functions stopped working: — MRCA(), geom_hilight(), and geom_cladelab() I have searched the web for answers. Example: > sessionInfo( ) R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4.1 Matrix products: default BLAS:…

How refget works. Credit: Stephanie Li / GA4GH A widely-used tool that finds the exact references needed to pinpoint differences in our DNA just got a refresh. On 17 July, the Standards Steering Committee of the Global Alliance for Genomics and Health (GA4GH) voted to release refget v2.0. With better…

I was working on a project when RStudio suddenly gave an Error message, which would disappear on restart. I tried to uninstall and reinstall, but the problem persisted. I just switched to Mac so I am not well versed in the OS. Does anybody have any ideas? R Session Startup…

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

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/beefy18/data/main-amd64-default/p8fb94260154e_s510fd83138/logs/viennarna-2.5.1.log Build URL: pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p8fb94260154e_s510fd83138 Log: =>> Building biology/viennarna build started at Sat Jul 15…

About a month ago, I updated R and Rstudio and downloaded Rtools. I had trouble getting rstan to run, and somehow messed up Rstudio so it can’t find libraries. When I open Rstudio, I get the error: During startup – Warning message: package ‘stats’ in options(“defaultPackages”) was not found Error…

R program 0 Hi, when I’m trying to install.packages in R program I always face with this Error: package or namespace load failed for ‘ggplot2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘colorspace’ how can i fix this? error Rprogram install.packages • 34 views •…

You can use Smithy, an interface definition language (IDL) to model your APIs. To use Smithy, in TypeSafeApiProject, specify it as your model.language. TSJAVAPYTHON new TypeSafeApiProject({ model: { language: ModelLanguage.SMITHY, options: { smithy: { serviceName: { namespace: ‘com.mycompany’, serviceName: ‘MyApi’, }, }, }, }, … }); TypeSafeApiProject.Builder.create() .model(ModelConfiguration.builder() .language(ModelLanguage.SMITHY) .options(ModelOptions.builder()…

We’re excited to share with you a new library called Keras Core, a preview version of the future of Keras. In Fall 2023, this library will become Keras 3.0. Keras Core is a full rewrite of the Keras codebase that rebases it on top of a modular backend architecture. It…

Dear Community,(Disclaimer : I learned R two weeks ago so most probably a very nooby question)I have run the follwing code to install DESeq2 based on the advice of my Post-Doc: BiocManager::install(c(“DESeq2″,”EnhancedVolcano”,”apeglm”)) Everything seemed fine except for DESeq2 where I had an issue with dependcy for the “RCurl” package that…

DESeq2, Timecourse using fitted splines 0 @2289c15f Last seen 7 hours ago Germany Hello, I am analyzing timecourse data of aging thymus samples. 29 samples, 11 different age groups. I am fitting splines for each gene and running LRT. Is there a more reliable way to tell how many degrees…

joyplenet (태희 김) July 5, 2023, 1:46am 1 hi, I want to train/test and generate jit::script structure totally in C++ code.simply, I want to trace modules implemented in totally libtorch C++.Always torch provides save script in python and load script in C++. But, I want to use script in C++…

I wanted to use the packages ggplot2 and interactions. I first installed interactions and then ggplot2. However I got error messages because I did not have the newest version of ggplot2.I tried updating ggplot2, which repeatedly did not work. So I deinstalled it and tried reinstalling it. Now I can’t…

Hi I would like to update my R version but an errors occurs. Could I ask for help regarding to this, please? Thank you in advance! Here is the error. install.packages(“installr”) Installing package into ‘/home/ss2826/R/x86_64-pc-linux-gnu-library/4.0’ (as ‘lib’ is unspecified) trying URL ‘cran.rstudio.com/src/contrib/installr_0.23.4.tar.gz&#8217; Content type ‘application/x-gzip’ length 158533 bytes (154 KB)…

Hello, I have a question about the complex study design in the R ALDEx2 package (bioconductor.org/packages/devel/bioc/vignettes/ALDEx2/inst/doc/ALDEx2_vignette.html#46_Complex_study_designs_and_the_aldexglm_module). My goal is to compare more than two groups (e.g. two or more treatments vs control). In a simple case with two groups, we use a vector with two groups: data(selex) #subset only the…

A minimal demo: — title: “demo” lang: zh knitr: opts_chunk: collapse: false format: gfm: default — 第一行 第二行 – 第三行 – 第四行 – 第五行 The output # demo 第一行二行 第三行 第四行 第五行 However, the expected output is # demo 第一行 第二行 – 第三行 – 第四行 – 第五行 There are more…

I’m trying to give users access between servers within a namespace.If everything works with external servers (hub, postgres, openssh-server), then how to get access from these servers to pod singleuser ?Or get access from one user to another. i started latest default config server with singleuser: startTimeout: 30 image: pullPolicy:…

Hi all ! For some reason I cannot install ggplot2 on my R studio (Version 4.0.3) I installed Rtools 4 and restarted R and I input the following command : write(‘PATH=”{RTOOLS40_HOME}\\usr\\bin;{PATH}”‘, file = “~/.Renviron”, append = TRUE) Then I restarted R and I checked if the path was good :…

create the TFLite op One of the possible ways is to use pytorch2keras library. Post-training integer quantization with int16 activations. for TensorFlow Lite (Beta). In addition, I made some small changes to make the detector able to run on TPU/GPU: I copied the detect.py file, modified it, and saved it…

Like last time, I deleted my previous versions of R but I still don’t get the prompt. You need to set your library path to a folder that exists. Error in print(nycflights13) : object ‘nycflights13’ not found, Tried restarting and updating r and r studio both. Heres how to do…

IsoformSwitchAnalyzeR Error in reading GTF file 0 Hi, I am using IsoformSwitchAnalyzeR v1.21.0 in R 4.3.0 environment using RStudio (2023.06.0+421 “Mountain Hydrangea” Release). When I try to import GTF file (obtained from Ensembl Plants) I get the following error ; Step 1 of 7: Checking data… Step 2 of 7:…

I followed the tutorial to the letter and made a functioning jupyter-hub instance with the helm chart. I setup a hostname on /etc/hosts so I didn’t need to write the ip every time I entered the server. Later I followed the guide to setup https (because I thought it was…

VariantFiltering error 0 @andrew-beggs-5579 Last seen 15 hours ago United Kingdom Hi Trying to run VariantFilter, manage to import fine, PED file is pretty standard: FAM001 SAMPLE_C SAMPLE_P1 SAMPLE_P2 1 2 FAM001 SAMPLE_P1 0 0 0 1 FAM001 SAMPLE_P2 0 0 0 1 > vfpar VariantFiltering parameter object VCF file(s):…

Hello Experts. I am getting the following error when I try to load the reticulatepackage I built in a local conda environment: Error: package or namespace load failed for ‘reticulate’ in dyn.load(file, DLLpath = DLLpath, …): unable to load shared object ‘~/Gits/nlp_r_in_python_testing/nlp_py_env/lib/R/library/reticulate/libs/reticulate.so’: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20′ not found (required by ~/Gits/nlp_r_in_python_testing/nlp_py_env/lib/R/library/reticulate/libs/reticulate.so)…

Additional Inherited Members  Public Attributes inherited from gmx::test::MdrunTestFixture SimulationRunner  runner_   Helper object to manage the preparation for and call of mdrun.    Public Attributes inherited from gmx::test::IntegrationTestFixture ::gmx::test::TestFileManager  fileManager_   Object that manages finding input files, writing temporary output files and cleaning up files.    Protected Member Functions inherited…

I’m trying to create a plot showing the abundance of ASVs within control vs true samples. This isn’t an issue with the code since I’ve used it before and it was just working yesterday, but I’ll include it here: # Starting from a phyloseq object called “noMitoChloroMock_physeq” # Set control…

using Microsoft.AspNetCore.Mvc.ApiExplorer; using Microsoft.AspNetCore.Mvc.Controllers; using Umbraco.Cms.Api.Common.OpenApi; namespace My.Custom.Swagger; public class MyOperationIdSelector : OperationIdSelector public override string? OperationId(ApiDescription apiDescription, ApiVersioningOptions apiVersioningOptions) // use this if you want to opt into the default Umbraco operation IDs: // return UmbracoOperationId(apiDescription, apiVersioningOptions); // only handle your own APIs here – make sure to let…

DESeq2 with nbinomGLM issues 0 @andrebolerbarros-16788 Last seen 6 hours ago Portugal Hi everyone, I was performing some DEGs and got this message: Warning messages: 1: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, … : the line search routine failed, possibly due to insufficient…

Sveltos, an open-source project, enables the deployment of Kubernetes add-ons across multiple clusters. It provides support for various deployment mechanisms such as Helm charts, kustomize resources, and resource YAMLs. With Sveltos, add-ons can be fetched from diverse sources for enhanced flexibility. When managing add-ons across numerous clusters, it becomes crucial…

bioconductor caches fails to load/corrupted for annotation databases 0 I’m unable to load annotation databases such as transcription databases due to corrupt caches. The problem still persists after reinstalling packages I tried following leads in this biconductor post but doesn’t solve the problem. Any suggestions would be gladly appreciated. Thanks…

Hello,Yesterday, I updated to the latest Rstudio version, but since then I am unable to make Rstudio start.I keep getting the following problem : R Session Startup Failure Report RStudio Version RStudio 2023.06.0+421 “Mountain Hydrangea ” (583b465e, 2023-06-05) for windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)…

This is a similar issue to this and this, but I have not been able to solve my case with the available information there. I am running qiime2 version 2023.2 in a conda environment. The problem was detected when I tried to run an analysis, but I could replicate the…

Hi! I’m trying to use GOATOOLS to perform Gene Ontology Enrichment analyses on a list of gene from a non-model organism (Anopheles gambiae, main vector of human malaria). I managed to run the tool, but i’m having issue with the statistical analyses since i’m not getting any output. I’m using…

Hello,I am new to using Git and would like to version my code within Rstudio. I have followed the below instructions (found here): In RStudio…• Open the project that you would like have associated with a GitHub Repository• Select Tools from the menu bar, then click on Version control, and…

boost/regex/v4/regex_token_iterator.hpp /* * * Copyright (c) 2003 * John Maddock * * Use, modification and distribution are subject to the * Boost Software License, Version 1.0. (See accompanying file * LICENSE_1_0.txt or copy at www.boost.org/LICENSE_1_0.txt) * */ /* * LOCATION: see www.boost.org for most recent version. * FILE regex_token_iterator.hpp *…

Used the following commands to install kubernetes and the jupyterhub 2.0.0 from helm chart:sudo snap install microk8s –classic –channel=1.27sudo usermod -a -G microk8s rootsudo chown -f –R root ~/.kubesudo usermod -a -G microk8s ziadminsudo chown -f -R ziadmin ~/.kubemicrok8s enable dnsmicrok8s enable hostpath-storagemicrok8s enable helm3microk8s enable metallb:10.0.54.200-10.0.54.220sudo systemctl enable iscsid.servicemicrok8s…

I receive an error every time I start RStudio (see below). I have tried reinstalling R and RStudio, and restarting my computer. The file path below in the error exists and is correct. R also works by itself. This error began after I updated macOS but I am not sure…

I was trying to deploy spark on kubernetes after some try and following this guide dev.to/akoshel/spark-on-k8s-in-jupyterhub-1da2 I successfully ran the example pi by using spark-submit from local system and it worked beautifully and I was able to see the pod in completed status. /opt/spark/bin/spark-submit \ –master \ –deploy-mode cluster…

This page details all the generators you can specify in your generators.yml. All of our generators are open source. ​fern-typescript-node-sdk Source code The TypeScript Node SDK generator outputs a fully functional TypeScript/JavaScript SDK for server-side usage. It can publish the SDK to npmjs.org (or any other npm repository). ​Config options…

Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

I have a project which uses spring framework 6 (not spring boot). I just used @RestController, so I can return any type of Object. Now I want to document these rest apis. And for this, I tried to use OpenAPI. I added implementation ‘org.springdoc:springdoc-openapi-ui:1.7.0 and other related dependencies also which…

OpenAPI Auto-Generated http-client Bindings to httpstan The library in lib provides auto-generated-from-OpenAPI http-client bindings to the httpstan API. OpenApi Version: 3.0.1 Installation Installation follows the standard approach to installing Stack-based projects. Install the Haskell stack tool. To build the package, and generate the documentation (recommended): stack haddock which will generate…

Your title asks about finding a function definition “in Python”. In code, this is perhaps what you want: import torch import source print(inspect.getsourcefile(torch.nn.Embedding)) source, start_line = inspect.getsourcelines(torch.nn.Embedding) print(start_line, start_line + len(source)) Output (for PyTorch 2.0.1): C:\Users\[redacted]\pytorch_test\Lib\site-packages\torch\nn\modules\sparse.py 13 224 However, most Python IDEs make this a lot easier. For example, if…

*Install.packages(“tidyverse”) and install.packages(“ggplot2”) fails with non-zero exit status. I’ve tried using install.packages(“tidyverse”) and install.packages(“ggplot2”) but both ends in non-zero exit status. Part of the error reads Error i loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘rlang’ 1.0.2 is being loaded, but >= 1.0.6 is required I’ve tried to remove.packages(“rLang”)…