Tag: cran

CRAN Package Depends on Bioconductor Package Installing error

In R 3.0.2, the following works: At the time of this writing, the value ind can take a vector with values between 1 and 8, and the following meaning: 1: CRAN 2: BioC software 3: BioC annotation 4: BioC experiment 5: BioC extra 6: Omegahat 7: R-Forge 8: rforge.net This…

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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Installing Bioconductor packages error –> Error in readRDS(dest) : error reading from connection

I have been trying to install Bioconductor in R (version 4.0.5). Each time I try to insert the following code, I get some error like: >if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(version = “3.12”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: CRAN.csiro.au/ Bioconductor version 3.12…

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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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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

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R ggpmisc::ggplot — EndMemo

R ggplot — ggpmisc ggplot() initializes a ggplot object. It can be used to declare the input spectral object for a graphic and to optionally specify the set of plot aesthetics intended to be common throughout all subsequent layers unless specifically overridden. ggpmisc::ggplot is located in package ggpmisc. Please install…

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

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

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Index of /contrib/main/00Archive/SNPRelate

Name Last modified Size Description Parent Directory   –   SNPRelate_0.9.0.tar.gz 2011-08-03 06:26 3.1M   SNPRelate_0.9.1.tar.gz 2011-08-13 13:04 3.1M   SNPRelate_0.9.2.tar.gz 2012-02-02 07:30 1.1M   SNPRelate_0.9.3.tar.gz 2012-03-05 07:20 1.1M   SNPRelate_0.9.4.tar.gz 2012-03-17 09:18 1.1M   SNPRelate_0.9.5.tar.gz 2012-04-25 04:39 1.1M   SNPRelate_0.9.6.tar.gz 2012-07-22 06:19 1.5M   SNPRelate_0.9.7.tar.gz 2012-08-30 05:14 3.0M  …

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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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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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[Bug 1951032] Autopkgtest regression report (glibc/2.31-0ubuntu9.4)

All autopkgtests for the newly accepted glibc (2.31-0ubuntu9.4) for focal have finished running. The following regressions have been reported in tests triggered by the package: snapd-glib/1.58-0ubuntu0.20.04.0 (armhf) apt/2.0.6 (armhf) libmath-mpfr-perl/4.13-1 (armhf) art-nextgen-simulation-tools/20160605+dfsg-4 (armhf) ruby-nokogiri/1.10.7+dfsg1-2build1 (armhf) r-cran-rgdal/1.4-8-1build2 (armhf) arrayfire/3.3.2+dfsg1-4ubuntu4 (armhf) libpango-perl/1.227-3build1 (armhf) libimage-sane-perl/5-1 (s390x) ruby-bootsnap/1.4.6-1 (arm64) mle/1.4.3-1 (ppc64el, arm64) libsyntax-keyword-try-perl/0.11-1build1 (armhf)…

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Description, Programming Languages, Similar Projects of Rbert

RBERT is an R implementation of the Python package BERT developed at Google for Natural Language Processing. Installation You can install RBERT from GitHub with: # install.packages(“devtools”) devtools::install_github( “jonathanbratt/RBERT”, build_vignettes = TRUE ) TensorFlow Installation RBERT requires TensorFlow. Currently the version must be <= 1.13.1. You can install it using…

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Virtual environment in R? – Stackify

I’m going to use the comment posted by @cboettig in order to resolve this question. Packrat Packrat is a dependency management system for R. Gives you three important advantages (all of them focused in your portability needs) Isolated : Installing a new or updated package for one project won’t break…

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Install package without updating dependent package

Install package without updating dependent package 1 @23c4e923 Last seen 18 hours ago Japan Hi, I’m trying to install AnnotationForge, and it is said that the package “Matrix” is old. > BiocManager::install(“AnnotationForge”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16),…

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Bioconductor URI, fallback and time-machine

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

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CRAN Package Check Results for Package chromoMap

CRAN Package Check Results for Package chromoMap CRAN Package Check Results for Package chromoMap Last updated on 2021-12-08 03:58:15 CET. Check Details Version: 0.3.1 Check: dependencies in R code Result: NOTE     Namespace in Imports field not imported from: ‘htmltools’     All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK, r-release-macos-arm64,…

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CRAN – Package ggmatplot

CRAN – Package ggmatplot ggmatplot: Plot Columns of Two Matrices Against Each Other Using ‘ggplot2’ A quick and easy way of plotting the columns of two matrices or data frames against each other using ‘ggplot2’. Although ‘ggmatplot’ doesn’t provide the same flexibility as ‘ggplot2’, it can be used as a…

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RStudio AI Weblog: Please permit me to introduce myself: Torch for R

Final January at rstudio::conf, in that distant previous when conferences nonetheless used to happen at some bodily location, my colleague Daniel gave a chat introducing new options and ongoing growth within the tensorflow ecosystem. Within the Q&A component, he was requested one thing sudden: Have been we going to construct…

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r-bioc-basilisk — Freezing Python Dependencies Inside Bioconductor Packages

On Sun, Sep 19, 2021 at 03:45:57PM -0500, Dirk Eddelbuettel wrote: > > | I’m thinking about a “fake-basilisk” like r-cran-bh or r-bioc-zlib. > > I had a similar thought. I am also friends with the author of it. > > They are doing ‘The Right Thing’ there for _their_…

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Bug#991859: BioConductor MOFA2 needs basilisk

Hi Dirk, On Sun, Sep 19, 2021 at 03:45:57PM -0500, Dirk Eddelbuettel wrote: > > | I’m thinking about a “fake-basilisk” like r-cran-bh or r-bioc-zlib. > > I had a similar thought. I am also friends with the author of it. > > They are doing ‘The Right Thing’ there…

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Classifiers for predicting coronary artery disease

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

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Sql Server Import From Excel With Sql, Duplicate Column Names

Explore LabKey Server’s specialized tools for assay data management below and read additional documentation on the LabKey support and documentation portal. Flow. Using SQL Search you can search for the column name and find all the stored procedures where it is used. Work faster. Finding anything in the Object Explorer….

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how to install packages in r

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

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Bioconductor API Bump to 3.13

Hi Andreas, On 26-08-2021 07:45, Andreas Tille wrote: > Hi Dylan, > > On Sun, Aug 15, 2021 at 01:17:29PM +0200, Andreas Tille wrote: >> Hi, >> >> On Sun, Aug 15, 2021 at 10:01:21AM +0200, Dylan Aïssi wrote: >>> >>> The transition tracker is on at >>> release.debian.org/transitions/html/r-api-bioc-3.13.html >>>…

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Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

1. Thompson, J. N. & Pellmyr, O. Evolution of oviposition behavior and host preference in Lepidoptera. Annu. Rev. Entomol. 36, 65–89 (1991). Article  Google Scholar  2. Bowers, M. D. Iridoid glycosides and host-plant specificity in larvae of the buckeye butterfly, Junonia coenia (Nymphalidae). J. Chem. Ecol. 10, 1567–1577 (1984). CAS …

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install GenomicFeatures fail

install GenomicFeatures fail 1 @5b9023e7 Last seen 19 hours ago China BiocManager::install(‘GenomicFeatures’) results show ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) ‘GenomicFeatures’ also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’ Packages which are only…

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issues installing pathfindR package

issues installing pathfindR package 1 Hi I am trying to use the pathfindR package to do enrichment analysis on my data. According to the vignette the package is downloaded from CRAN by install.packages(“pathfindR”) this gives the following output Installing package into �� (as �lib� is unspecified) Warning in install.packages :…

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working with .gmt files

working with .gmt files 3 Hi! I have downloaded a pathway data set in .gmt format form the GSEA website. I’m wondering how can I properly read this data set in R. Could anyone help me? Thank you!   myposts • 9.5k views • link updated 2 hours ago by…

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