Tag: NAMESPACE

What’s New in IntelliJ IDEA Ultimate 2023.3

Releases The Ultimate edition of IntelliJ IDEA goes beyond the basics, offering a comprehensive suite of features, including in-depth profiling capabilities, database tools, built-in support for many web and enterprise frameworks, and more. In this latest v2023.3 release, we’ve rolled out a suite of new features to enhance your coding…

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Deploying OpenAPI Helm Chart on AWS EKS

To deploy the OpenAPI Helm chart on AWS Elastic Kubernetes Service (EKS), we’ll follow these steps: Create an EKS cluster. Configure Kubeconfig to interact with your cluster. Use the Pulumi Kubernetes provider to deploy the OpenAPI Helm chart using kubernetes.helm.v3.Chart. Before we begin, ensure you have the following prerequisites in…

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Deleting a column from data frame and then running DESeq2

Forgive me if this post is messy, I’m new to this! I’m analyzing RNA Seq data and found that one of my samples is an outlier (sample AV17). I’m trying to exclude it from my analysis, but whenever I do, using this code: dds = subset(countData, select = -c(AV17) ),…

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Having Trouble Loading Required Packages : Lazy-Load database is corrupt – General

Hi, I am very new to R-Studio but a few months I had taken an 8-week course in which I was taught to use R-Studio for academic purposes. I recently decided to review some of the exercises we were provided with. However, I have now started to have trouble loading…

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Gromacs: gmx::test::anonymous_namespace{observablesreducer.cpp}::Subscriber Class Reference

This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Helper class that models an MD module that needs to make a subscription to ObservablesReducer. static constexpr int  s_subscriberBufferMinimumSize = 3   Ensure that each subscriber sends an interesting amount of data.   static…

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Error In Library(Shiny) ‘Shiny’ Is Not A Valid Installed Package at David Lord blog

Error In Library(Shiny) ‘Shiny’ Is Not A Valid Installed Package. However, not sure i get this message. Package or namespace load failed for shiny : shiny upload file example “Error an error had occured. Check your – image credit : community.rstudio.com It means that…

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gcc – Error compiling giac (inside SageMath) in poly.h function

Environment: CentOS 7.9 GCC 13.1.0 SageMath 10.0 When compiling SageMath, the compilation gets to the “giac” program and fails. The failure occurs in the “poly.h” function. I’m on a closed network so I cannot upload the logfile. Here is the last part of the error: modpoly.cc:16082:1: internal compiler error: Aborted…

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Error in calculating inter-individual divergence / spread

Hi all I am currently facing an issue while working with the microbiome package in R and would greatly appreciate your insights. > b.lgg <- divergence(subset_samples(physeq, Description == “Stool_controls”), + apply(abundances(subset_samples(physeq, Description == “Stool_controls”)), 1, median)) > b.pla <- divergence(subset_samples(physeq, Description == “Stool_samples”), + apply(abundances(subset_samples(physeq, Description == “Stool_samples”)), 1, median))…

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

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

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Loading R Packages In RStudio: A Step-By-Step Approach

Article Summary Box Preparing RStudio for package management is pivotal, involving setting up workspace directories and ensuring R version compatibility for optimal package functionality. In Understanding Package Libraries, the intricacies of library paths and package storage locations reveal strategies for streamlined package accessibility and organization. Advanced Techniques for Package Loading…

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pytorch-cluster: FTBFS: ImportError: Failed to load PyTorch C extensions:

Source: pytorch-cluster Version: 1.6.1-2 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu…@debian.org Usertags: ftbfs-20231212 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > debian/rules clean > dh clean –buildsystem pybuild > dh_auto_clean -O–buildsystem=pybuild > I: pybuild…

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removeBatchEffect with non-linear model fit

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

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cluster – Slurm nodes randomly dropping

I’ve set up a cluster using Slurm, consisting of a head node, 16 compute nodes, and an NAS with NFS-4 network shared storage. I’ve recently installed Slurm on Ubuntu v22 via apt (sinfo -V reveals slurm-wlm 21.08.5). I’ve tested with some single-node and multi-node jobs, and I can get jobs…

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[F] getOpenAPITypeName | TypeSpec

getOpenAPITypeName( program, type, options, existing?): string Gets the name of a type to be used in OpenAPI. For inlined types: this is the TypeSpec-native name written to x-typespec-name. For non-inlined types: this is either the friendly name or the TypeSpec-native name. TypeSpec-native names are shortened to exclude root TypeSpec namespace…

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How can I force operator available when statically linking? – C++

I’m building a program that utilizes libtorch to perform inference using static libs. Things work alright if I link libtorch_cpu.a using the whole-archive approach, but I need to be able to build without whole-archive. In the case without whole-archive, the build process succeeds, but I get an error at runtime…

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ScRNAseq analysis scran :: quickcluster Error

ScRNAseq analysis scran :: quickcluster Error 1 @d4a334e3 Last seen 15 hours ago Germany Hello! I am having an error while doing normalization for my scRNAseq data, I would appreciate the help of anyone who countered the same problem the error is during quickcluster command as follow: clust <- quickCluster(sce)…

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Bioconductor Code: SigCheck

 About browsing: devel Branches RELEASE_3_0 RELEASE_3_1 RELEASE_3_10 RELEASE_3_11 RELEASE_3_12 RELEASE_3_13 RELEASE_3_14 RELEASE_3_15 RELEASE_3_16 RELEASE_3_17 RELEASE_3_18 RELEASE_3_2 RELEASE_3_3 RELEASE_3_4 RELEASE_3_5 RELEASE_3_6 RELEASE_3_7 RELEASE_3_8 RELEASE_3_9 devel Files Commits Stats Network Graph SigCheck Clone ZIP TAR × SSH HTTPS Name Mode Size R 040000 data 040000 inst 040000 man 040000 vignettes 040000 DESCRIPTION…

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Rstudio Starting fatal error – General

I failed to start Rstudio:here is the error: R Session Startup Failure Report RStudio Version RStudio 2023.09.1+494 “Desert Sunflower ” (cd7011dc, 2023-10-16) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.09.1+494 Chrome/116.0.5845.190 Electron/26.2.4 Safari/537.36 Error message [No error available] Process Output The R session exited…

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Genetic risk converges on regulatory networks mediating early type 2 diabetes

Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article  ADS  PubMed  Google Scholar  Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…

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Package Prefix double-colon notation in user-created package – Package development

Our team created a user-defined R package for a project. When we created this package, we did so on a Windows OS and included the name of the package we built as a prefix whenever we call one of its R functions (e.g., dplyr::filter()). However, now that our RStudio server…

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Bioconductor Code: daMA

 About browsing: devel Branches RELEASE_1_4 RELEASE_1_5 RELEASE_1_6 RELEASE_1_7 RELEASE_1_8 RELEASE_1_9 RELEASE_2_0 RELEASE_2_1 RELEASE_2_10 RELEASE_2_11 RELEASE_2_12 RELEASE_2_13 RELEASE_2_14 RELEASE_2_2 RELEASE_2_3 RELEASE_2_4 RELEASE_2_5 RELEASE_2_6 RELEASE_2_7 RELEASE_2_8 RELEASE_2_9 RELEASE_3_0 RELEASE_3_1 RELEASE_3_10 RELEASE_3_11 RELEASE_3_12 RELEASE_3_13 RELEASE_3_14 RELEASE_3_15 RELEASE_3_16 RELEASE_3_17 RELEASE_3_18 RELEASE_3_2 RELEASE_3_3 RELEASE_3_4 RELEASE_3_5 RELEASE_3_6 RELEASE_3_7 RELEASE_3_8 RELEASE_3_9 devel Files Commits Stats Network Graph…

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Why is DMRcate not available for Bioconductor version 3.18?

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

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Resolving Slurm cgroups Plugin Errors on Ubuntu 22.04 Nodes

I’m working with Slurm and facing issues specifically with the cgroups plugin on Ubuntu 22.04 nodes. Our team is relatively new to Slurm, and we’ve been trying to optimize our resource management for complex computing tasks. However, we’ve encountered a series of errors that are proving difficult to resolve. Here’s…

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Troubleshooting Slurm cgroups Plugin on Ubuntu 22.04

I’m facing a challenging issue with the Slurm cgroups plugin on a system running Ubuntu 22.04. We’re relatively new to Slurm and started using it for better resource management in complex computing tasks. However, we’ve hit a snag with the cgroups plugin, particularly on our Ubuntu 22.04 nodes. Here’s what…

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RStudio For Quantitative Finance

Introduction to RStudio R is widely used in quantitative finance due to its extensive statistical capabilities, data manipulation tools, and its active community that develops and maintains specialized packages for finance. It offers a wide range of functionalities that enable professionals in the finance industry to analyze data, build models,…

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r-bioc-phyloseq 1.22.3-1

/usr/ root:root 0o755 /usr/lib/ root:root 0o755 /usr/lib/R/ root:root 0o755 /usr/lib/R/site-library/ root:root 0o755 /usr/lib/R/site-library/phyloseq/ root:root 0o755 /usr/lib/R/site-library/phyloseq/CITATION text/plain root:root 0o644 606 bytes /usr/lib/R/site-library/phyloseq/data/ root:root 0o755 /usr/lib/R/site-library/phyloseq/data/datalist text/plain root:root 0o644 44 bytes /usr/lib/R/site-library/phyloseq/data/enterotype.RData application/x-xz root:root 0o644 190.7 KB /usr/lib/R/site-library/phyloseq/data/esophagus.RData application/x-xz root:root 0o644 1.8 KB /usr/lib/R/site-library/phyloseq/data/GlobalPatterns.RData application/x-xz root:root 0o644 425.4 KB /usr/lib/R/site-library/phyloseq/data/soilrep.RData application/x-xz root:root 0o644 104.9 KB /usr/lib/R/site-library/phyloseq/DESCRIPTION text/plain…

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Help! RStudio starts to a blank screen after update; clean install worked, but not after time machine backup. – RStudio IDE

Error Information: Description of issue – After updating to OS Sonoma, RStudio is a blank window. I only see the name of the toolbar. There are no options in the toolbar either, it says empty. R app works fine. Attempted steps taken to fix –Reinstalled appsReinstalled OS system sonoma (didn’t…

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Testing an OpenAPI specification in PHP

Introduction OpenAPI has become the de facto standard for API specifications. According to its description, “It is a specification language for HTTP APIs that defines structure and syntax in a way that is not wedded to the programming language the API is created in”. The specification is independent of the…

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Rstudio cant install packages – General

Hi together i am currently doing an introductory course in R but having trouble with Rstudio.i want to install a package but just get a really, really long error.Below is what i get in return but i’m already struggling to understand the first bit because i have got rtools installed…

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How to make OpenAPI codegen understand that it is necessary to decode an XML and not a JSON response into reusable data in PHP during generation?

I’m trying to generate my openapi.yaml specification : openapi: 3.0.3 info: title: OpenAPI 3.0 description: |- This is a sample Server based on the OpenAPI 3.0 specification. You can find out more about Swagger at [https://swagger.io](https://swagger.io). contact: email: [email protected] version: 1.0.11 externalDocs: description: Find out more about OpenAPI Codegen url:…

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Building Pytorch for Conda from source with GLIBCXX_USE_CXX11_ABI=1

GdMacmillan (Gordon MacMillan) November 26, 2023, 4:17pm 1 Before I begin, I’ve checked the topics similar to this one and they all have linking issues and PR’s that are outdated. I am attempting to compile the libtorch binaries and build pytorch from source with GLIBCXX_USE_CXX11_ABI=1 The reason for this, I…

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R freezing when I create a simple plot – General

Hello! My issue is similar than the one discussed: Running even a simple plot command triggers never-ending stop sign. Only resolution is hitting the stop button several times to abort. The following freezes the session: x <- c(1,2,3) y <- c(1,2,3) plot(x,y) > sessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0…

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RStudio session failed to start – RStudio IDE

Error Information: Description of issue –I’ve used RStudio for many years without problem. I was using it yesterday without problem; then, it crashed and won’t restart. I’ve reinstalled R and RStudio. I believe that I have removed RStudio state files. Attempted steps taken to fix – System Information: RStudio Edition:…

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Rstudio crashes just before producing a brms model – General

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

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Spring boot (Open API issue)

Spring boot (Open API issue) – Stack Overflow Asked today Viewed 12 times Following is the error: Plugin [id: ‘org.springdoc.openapi-gradle-plugin’, version: ‘1.5.0’] was not found in any of the following sources: Run with –info or –debug option to get more log output. Run with –scan to get full insights. Exception…

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open-solid/open-api-bundle – Packagist

Provides a tight integration of the famous zircote/swagger-php library into the Symfony full-stack framework for generating OpenAPI documentation and building Restful APIs quickly. This bundle is especially created for API-First development. Installation composer require open-solid/open-api-bundle Import the Swagger controller routes in config/routes.yaml: openapi: resource: ‘@OpenApiBundle/config/routes.php’ Basic Usage Create a controller…

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JupyterHubSingleUser – Failed to connect to my Hub at http://127.0.0.1:8081/hub/api – JupyterHub – Jupyter Community Forum

After updating the base notebook image to Quay (base-notebook:2023-10-31) getting these connection errors in single user server spawn. Earlier used version jupyter/base-notebook:2023-04-14 this working without any errors. (python3.10 version used in working docker image) Environment:Used helm chart version “3.0.3” to deploy the 4.0.2 version of application on AWS EKS Cluster….

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Trying to spawn pods in other namespace – Zero to JupyterHub on Kubernetes

Hello manics, thank you for your quick response and the tips on further debugging!In the default setting everything works fine, I can even use a profile as long as I dont use the kubespawner_override.namespace option. Here are the logs from the profile+namespace setting with the debug logging:Hub: [I 2023-11-16 19:58:45.827…

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DESeq2 design with unbalance data and a multifactor design

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

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DESeq2 with unbalanced dataset and multifactor design

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

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Improve setting up docs – ExecuTorch

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

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Integrating ASP.NET Core OpenAPI For Efficient Development

Embracing ASP.NET Core and its integration with OpenAPI can significantly streamline the process of building and documenting web APIs. This synergy allows you to automatically generate interactive API documentation and client SDKs, ensuring that your development workflow remains both robust and efficient. 📌 With this approach, maintaining up-to-date documentation becomes…

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JupyterHub on Kubernetes cannot failed to cull user pods

I implemented JupyterHub using a Helm chart on a local Kubernetes cluster on VMware virtual machines. I want to cull users after they have been inactive for a while, but it seems not to work. This error log from the hub pod (pod named hub-545895f988-vmj2k) might be related: [W 2023-11-09…

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cTrader Forum – New to cTrader OpenAPI, help please.

New to cTrader OpenAPI, help please. 08 Nov 2023, 21:05 Hello,I’m experienced in cAlgo, but new to cTrader OpenAPI.  I’ve followed the Registering a New Application and got Credentials, I also installed the SDK package. Now I want to build a connection and get some of my account basic information…

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Fatal error – Running lmer – General

Hi! I am a beginner trying to model microbiome alpha diversity in Rstudio, and have been stuck, as every time I try to run the lmer function in Rstudio, R aborts and terminates my session. I have tried updating R, updating packages, removing and re-installing packages, and detaching packages that…

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Real-time collaboration for jupyterhub – Zero to JupyterHub on Kubernetes

Hi there,I’ve been playing around with RTC extension on jupyterhub recently and I’ve been stuck at creating-collaboration-accounts for a while. It mentions This configuration code runs when jupyterhub starts up, so I included the example code block under hub.extraConfig.’myConfig.py’, then I got this error: TypeError: ‘LazyConfigValue’ object is not subscriptable….

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Trying to upgrade jupyterhub from helmchart 2.0.0 to 3.1.0 – Zero to JupyterHub on Kubernetes

Hello, I’ve been trying to upgrade helmchart from 2.0.0 to the latest 3.1.0 (speaking as of date 8 Nov. 2023) on k8s (v1.25) AWS cluster. I got this error message when I check the logs of helmrelease Last Helm logs: Patch Deployment “hub” in namespace jupyterhub Patch Deployment “proxy” in…

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Import a Bioconductor package that is only used in a vignette/.Rmd script

My Bioconductor package is receiving Errors about a package not existing. I have an R package with Bioconductor. In the vignettes folder, I have several .Rmd files that have the following chunk at the top: title: ‘Manuscripts’ package: pkgName bibliography: pkgName.bib output: **BiocStyle**::html_document: toc_float: true tidy: TRUE border-width: 5px vignette:…

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In CMake for CUDA developent, how can I control gencode options?

I am configuring the project using CMakeLists.txt generated nvcc compile options for gencode, it contains almost all the arch options like the below. -gencode arch=compute_52,code=sm_52 -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 -gencode arch=compute_70,code=sm_70 -gencode arch=compute_75,code=sm_75 -gencode arch=compute_80,code=sm_80 -gencode arch=compute_86,code=sm_86 -gencode arch=compute_90,code=sm_90 -gencode arch=compute_90,code=compute_90 I want only -gencode arch=compute_80,code=sm_80 How can I prevent…

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Why is R-Studio Only Showing Comments from Some Package Functions, but not all? – RStudio IDE

I’ve noticed that there may be a new feature on the latest version of R Studio on Ubuntu 22.04, but I can’t seem to find any news about it and I don’t know what to search on Google to understand it more. Here is my R Studio Version RStudio 2023.09.1+494…

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different results with and without releveling when providing contrast

Hello, I am conducting a differential expression analysis of RNA-seq data where I have samples from three treatment doses (control, low, high) at three developmental timepoints (W6, W8, GS45). Note these are not paired samples (i.e. different individuals sampled at each timepoints). I am interested in differentially expressed genes caused…

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Having trouble importing PyTorch as an external package – Coding

OS: Mac 13.6PsychoPy v2023.2.1 Hello, I have been attempting to install PyTorch as an external module into PsychoPy but have found no luck. I have installed PyTorch into /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages And pasted this path into PsychoPy Preferences When I try to run the code I receive this error message: ImportError: Failed…

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couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘

Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…

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Building multi-tenant JupyterHub Platforms on Amazon EKS

Introduction In recent years, there’s been a remarkable surge in the adoption of Kubernetes for data analytics and machine learning (ML) workloads in the tech industry. This increase is underpinned by a growing recognition that Kubernetes offers a reliable and scalable infrastructure to handle these demanding computational workloads. Furthermore, a…

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Error in Gviz (actually, rtracklayer)

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

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Gromacs: gmx::ILogTarget Class Reference

#include <gromacs/utility/logger.h> Inherited by gmx::LogTargetCollection, gmx::LogTargetFormatter, and gmx::test::anonymous_namespace{loggertest.cpp}::MockLogTarget. Target where log output can be written. virtual void  writeEntry (const LogEntry &entry)=0   Writes a log entry to this target.   The documentation for this class was generated from the following files: src/gromacs/utility/logger.h src/gromacs/utility/logger.cpp Read more here: Source link

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Accessing a Google Storage Bucket mounted as a Persistent Volume – Zero to JupyterHub on Kubernetes

That’s good to know; probably means my error is somewhere in my config. I’ll try to dump the relevant settings. Output of kubectl get pod while starting a jupyterhub user server: NAME READY STATUS RESTARTS AGE continuous-image-puller-972b7 1/1 Running 0 24m continuous-image-puller-tz5ls 1/1 Running 0 26h gcs-fuse-csi-static-pvc 2/2 Running 0…

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[slurm-users] job_container/tmpfs and rootless apptainer

Hi, I was wondering if some light could be shed as to why permissions on the mounted /tmp need to be 700 when using the job_container/tmpfs plugin. I’m asking this because we are considering allowing for users to run rootless apptainer as a method for building containers from a slurm…

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Annotation hub and clusterProfiler errors

Annotation hub and clusterProfiler errors 1 @33343537 Last seen 4 hours ago Norway How can I get AnnotationHub() run? Also, clusterProfiler is not working because I am unable to install HPO.db > ah <- AnnotationHub() **Error in `collect()`: ! Failed to collect lazy table. Caused by error in `db_collect()` >…

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r – Issues with rqa in nonlinearTseries version 0.2.12 in RStudio

I am trying to run a simple rqa using nonlinearTseries in R using version 0.2.12 of the library a <- c(1,2,1,2,1,2) a.rqa <- rqa(time.series = a, embedding.dim = 1, time.lag = 1, radius = .1) While I never had any issue with this in the past, I noticed that since…

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Issue Running Exported R Script in RStudio: ‘clean_data_frame’ Not Found in ‘namespace:exploratory’ – Issues

Problem When attempting to run an R Script for data wrangling exported from Exploratory, you may encounter the following error in RStudio: Error: ‘clean_data_frame’ is not an exported object from ‘namespace:exploratory’ Solution To resolve this issue, follow these steps: Avoid Modifying .libPaths: Do not set the .libPaths in your Rprofile.site…

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

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/main-powerpc64le-default/pbc0e38d0f08e_s0afcac3e37/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=pbc0e38d0f08e_s0afcac3e37 Log: =>> Building misc/pytorch build started at Tue Oct 24…

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vanengers/php-openapi-client-generator – Packagist

Generate a PHP client for an OPENAPI specification Installation composer require –dev vanengers/php-openapi-client-generator Usage OPENAPI=http://127.0.0.1:8000/docs.json NAMESPACE=VendorName\\PackageName\\Generated OUTPUT_DIR=src/Generated ./bin/api-client-generator generate Specify the openapi specifications JSON file OPENAPI=http://127.0.0.1:8000/docs.json Specify the namespace for the generated classes NAMESPACE=VendorName\\PackageName\\Generated Specify the output directory for the generated classes OUTPUT_DIR=src/Generated Run the generator ./bin/api-client-generator generate Example client…

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Codegen Templates

Note: This information applies to SwaggerHub On-Premise. SwaggerHub On-Premise lets you upload custom Swagger Codegen modules for code generation. Custom generators will appear along with the built-in generators in the Export menu. They can be used in source control integrations. OpenAPI version compatibility SwaggerHub On-Premise 2.6.0 and later support custom…

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rtracklayer error for browserSession UCSC

rtracklayer error for browserSession UCSC 1 @f64e2e65 Last seen 16 hours ago Germany An older error from rtracklayer has resurfaced. When calling a browserSession, it gives the error below. I assume this is due to a URL problem, possibly when trying to connect to UCSC from Europe. Could someone please…

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Developing R/Bioconductor Packages for Genomics

Dear all, We are excited to announce our upcoming online course, “Developing R/Bioconductor Packages for Genomics” scheduled to take place from November 13 to November 17, 2023. In order to foster international participation, this course will be conducted online, making it accessible to learners from all over the world. Course…

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kableExtra bug only when using knit button in RStudio – RStudio IDE

I am currently unable to load the “kableExtra” package when using the “knit” button in RStudio. The code works fine if I execute it in the console or if I just call “rmarkdown::render” directly. I reported this bug previously, and the topic was closed after 21 days while I was…

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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files

Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…

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Plotting time series data after running natural splines regression in DESeq2.

Hello, I am running differential expression analysis on age-related changes in transcription using natural splines with DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) keep <- rowSums(counts(dds) >= 10) >= 3 dds <- dds[keep,] dds <- DESeq(dds, test=”LRT”, reduced =…

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OpenAPI models – FastAPI

FastAPI Reference – Code API OpenAPI OpenAPI Pydantic models used to generate and validate the generated OpenAPI. fastapi.openapi.models SchemaOrBool module-attribute SchemaOrBool = Union[Schema, bool] SecurityScheme module-attribute EmailStr Bases: str validate classmethod PARAMETER DESCRIPTION v TYPE: Any Source code in fastapi/openapi/models.py @classmethod def validate(cls, v: Any) -> str: logger.warning( “email-validator not…

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Overview of the language | Oxlip API Language

Table of contents Programs A program is a collection of statements. There are three types of statements: imports (use) declarations (let) resources (res) Statements only appear in the top-level scope of a program and end with a ;. Modules Modules are imported with the use keyword. Importing makes the variables…

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main-armv7-default][biology/viennarna] Failed for viennarna-2.6.3 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-armv7-default/p08943441f26e_s6e92fc9309/logs/viennarna-2.6.3.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p08943441f26e_s6e92fc9309 Log: =>> Building biology/viennarna build started at Mon Oct 16…

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I need help on my rstudio desktop – General

Please I need help installing tidyverse on my Rstudio desktop application. Been struggling with for more than 13 hours now yet to no avail. I installed the tidyverse package but when I input the library function to see the core tidyverse packages it tells me error. This is what I…

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R encountered fatal error when using processBismarkAln in methylKit

R encountered fatal error when using processBismarkAln in methylKit 2 Hi I am attempting to use methylkit to analyse my RRBS data but cannot seem to be able to import my files. I have .bam files generated from bismark. I read I can use function processBismarkAln to read these kind…

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Gromacs: gmx::test::anonymous_namespace{simd_math.cpp} Namespace Reference

Functions real  refInvsqrt (real x)   Function wrapper to evaluate reference 1/sqrt(x)   SimdReal gmx_simdcall  tstInvsqrtPair0 (SimdReal x)   Function wrapper to return first result when testing invsqrtPair.   SimdReal gmx_simdcall  tstInvsqrtPair1 (SimdReal x)   Function wrapper to return second result when testing invsqrtPair.   real  refSqrt (real x)  …

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yceruto/open-api-bundle – Packagist

Provides a tight integration of the famous zircote/swagger-php library into the Symfony full-stack framework for generating OpenAPI documentation and building Restful APIs quickly. This bundle is especially created for API-First development. composer require yceruto/open-api-bundle Import the Swagger controller routes in config/routes.yaml: openapi: resource: ‘@OpenApiBundle/config/routes.php’ Create a payload class with a…

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HW4.txt – /HW4 Due: 11:59pm Thursday March. 9 / Yanchen Li / SU Net ID: yli619 SUID:3922262852 /You are not allowed to use any helper

//HW4 Due: 11:59pm, Thursday, March. 9 // Yanchen Li // SU Net ID: yli619 SUID:3922262852 //You are not allowed to use any helper functions //You are not alllowed to use any extra class. #include <iostream> #include <map> #include <list> #include <tuple> using namespace std; class course { public: string name;…

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rstudio – How to ignore to install some R packages when building a new R package?

I am building a new R package using Rstudio. For one R function of my R package, I need to use another R package wrote by others. Generally, I have to list the R package in the row “Imports” of the file “DESCRIPTION”. Since this R function is not a…

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Windows 10: rstudio reticulate keras tensorflow :: anaconda vs. miniconda vs. python

The number of issues I’m having with a STABLE python environment operating beneath R/Rstudio is overwhelming… and the permutations of installation steps is far too flexible to inspire confidence with any approach. First, I used reticulate to uninstall_miniconda. I wiped the computer of any trace of python. I have updated…

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Bringing HPC and Large Scale AI onto Kubernetes : @VMblog

  SUNK, an implementation of Slurm on Kubernetes, will be made open-source in early 2024. Learn how it works. In the HPC and AI world, there are two kings: Slurm for scheduling and orchestrating massively parallel jobs and Kubernetes for running production applications like Inference. However, many companies face making…

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

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

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

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

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php – Nelmio/api-doc-bundle error: non-existent service “api_platform.openapi.normalizer” (Symfony 4)

I’ve a composer.json with these packages: “php”: “>=7.4”, “ext-xml”: “*”, “api-platform/core”: “^2.7”, “beberlei/doctrineextensions”: “1.0.19”, “doctrine/annotations”: “^1.0”, “doctrine/collections”: “~1.0”, “doctrine/doctrine-bundle”: “~1.4”, “doctrine/doctrine-migrations-bundle”: “^2.0”, “doctrine/event-manager”: “~1.0”, “doctrine/orm”: “^2.4.8”, “doctrine/persistence”: “~1.0”, “exercise/htmlpurifier-bundle”: “~3.0”, “fig/link-util”: “^1.0”, “nelmio/api-doc-bundle”: “4.11.1”, “nelmio/cors-bundle”: “^2.3”, “php-imap/php-imap”: “3.0.6”, “phpdocumentor/reflection-docblock”: “^5.3”, “predis/predis”: “^1.0”, “psr/cache”: “~1.0”, “psr/container”: “^1.0”, “psr/link”: “^1.0”, “psr/log”: “~1.0”,…

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extensions/openapi.go at test-cluster-bootstrap – extensions

// Package openapi provides primitives to interact with the openapi HTTP API. // // Code generated by entanglement.garden/egcli version (devel) DO NOT EDIT. package openapi import ( “fmt” “net/http” “entanglement.garden/common/httpx” “github.com/deepmap/oapi-codegen/pkg/runtimegithub.com/labstack/echo/v4 rts “github.com/ory/keto/proto/ory/keto/relation_tuples/v1alpha2 ) const ( EntanglementAuthScopes = “EntanglementAuth.Scopes” ) // Extension defines model for Extension. type Extension struct…

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DeSeq2 data comparison and extracting outputs

Hi, I have an RNA-seq experiment where there are 2 conditions and 2 genotypes. I am trying to figure out how to output the 2 conditions with 2 genotypes from the dds object. I have read online resources, however, it is still not clear what is extracted. I followed and…

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-ne in the terminal – RStudio IDE

After updating RStudio to 2023.09.0 Build 463 I have a strange -ne text appearing in the Terminal every time I hit enter. This -ne does not show up in my terminal or iterm. Anyone else experiencing this? > sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura…

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Model Your APIs With AWS Smithy

Smithy is an open source project by AWS with which you can model your APIs, generate code and documentation for clients and servers, as well as other artifacts, in many programming languages. Smithy sprung out AWS’s need of adopting a common format for its hundreds of APIs that would allow…

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Training NeMo Framework Models – NVIDIA Docs

You must prepare several datasets for the NeMo framework to use, depending on the type of model you are using. The Pile: NVIDIA provides utilities to download and prepare the Pile dataset. This dataset comprises 22 smaller datasets, blended by using the mix described in the paper The Pile:…

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Problems installing RMarkdown for R v2023.06.1 on a Mac – R Markdown

I’m having troubles installing RMarkdown for using knitr and publish my work, I’m using R Studio v2023.06.1 on a Mac with a macOS Monterey version 12.6.3. This is what I’m getting: install.packages(“knitr”)also installing the dependency ‘xfun’ There are binary versions available but the source versions are later:binary source needs_compilationxfun 0.30…

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Grafana Introduces ML Tool Sift to Improve Incident Response

Grafana Labs has introduced Sift, a feature for Grafana Cloud designed to enhance incident response management (IRM) by automating system checks and expediting issue resolution. Sift automates various aspects of incident investigation, including identifying error log patterns, detecting Kubernetes container crashes, spotting overloaded hosts, monitoring recent deployments, tracking resource contention,…

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Gromacs: gmx::analysismodules::anonymous_namespace{select.cpp}::IndexFileWriterModule Class Reference

Data module for writing index files. void gmx::analysismodules::anonymous_namespace{select.cpp}::IndexFileWriterModule::dataStarted ( AbstractAnalysisData *  data ) virtual Called (once) when the data has been set up properly. Parameters [in] data Data object to which the module is added. Exceptions APIError if the provided data is not compatible. unspecified Can throw any exception required…

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rstudio – Creating an R package using roxygen2. Issue with install.packages() , error in use_namespace()?

I have built a local package to handle some data manipulations that I commonly use. My file structure is: -RExample/ — adhoc.R — DESCRIPTION — man/ — function1.Rd — function2.Rd — NAMESPACE — R/ — src_code_1.R RExammple.Rproj Using oxygen2, I build the package: package_dir = “/direct/path/here/R/RExample/” build(package_dir, path=package_dir) The package…

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main-arm64-default][biology/viennarna] Failed for viennarna-2.6.3 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/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…

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Terminal will not start under Anaconda

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…

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boost/type_traits/integral_constant.hpp – 1.83.0

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))…

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Ninja: build stopped: subcommand failed. note: see declaration of ‘PyDict_GetItem’

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…

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Gromacs: anonymous_namespace{abstractoptionstorage.cpp}::MockOptionStorage Class Reference

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…

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Node.js 2023 Edition Available

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…

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Usage of the `singleuser.image.name` configuration – Zero to JupyterHub on Kubernetes

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…

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r – error when installing rgdal package on ubuntu 22.04, rstudio-sever 2023.06.02

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…

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