Hello, Use this. Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. Convince your IT department to relax the permissions for R packages Have you tried install.packages("locfit") ? Is there a proper earth ground point in this switch box? When an R package depends on a newer package version, the required package is downloaded but not loaded. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. so I would try to use BiocManager::install("XML"). Policy. Thanks! This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. Asking for help, clarification, or responding to other answers. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. I would recommend installing an older version of QIIME 2 for this plugin to work. I do know that it works well in qiime2-2020.6. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Documentation Making statements based on opinion; back them up with references or personal experience. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Any suggestions would be greatly appreciated. May be the version has problem How can I do ? March 1, 2023, 3:25pm Policy. Try again and choose No. 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in install.packages("BiocManager"), I get this error: Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called locfit, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy This article explains how to resolve the package or namespace loading error. rev2023.3.3.43278. https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6: https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip', User Agreement and Privacy Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 I've copied the output below in case it helps with troubleshooting. Is there a proper earth ground point in this switch box? [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R How to notate a grace note at the start of a bar with lilypond? Does a summoned creature play immediately after being summoned by a ready action? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): rev2023.3.3.43278. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Content type 'application/zip' length 386703 bytes (377 KB) [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 What am I doing wrong here in the PlotLegends specification? If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. How can we prove that the supernatural or paranormal doesn't exist? If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. Surly Straggler vs. other types of steel frames. Please read the posting (Factorization). [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Use of this site constitutes acceptance of our User Agreement and Privacy Is a PhD visitor considered as a visiting scholar? [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 binary source needs_compilation The error states that the current version is 0.4.5 but 0.4.10 is required. One solution is to find all available packages. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Thanks for contributing an answer to Stack Overflow! As such there are two solutions that may be more or less attainable given your own IT system. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' It only takes a minute to sign up. "4.2") and enter: For older versions of R, please refer to the appropriate or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. If I run install.packages(GenomeInfoDb) from R console, it is telling me that the package is not available for R version 3.5.1. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. What is a word for the arcane equivalent of a monastery? Is there anyone the same as mine error while loading library(DESeq2)? I tried again and again was met with missing packages BUT!!! [40] assertthat_0.1 rpart_4.1-10 nnet_7.3-12, It should not be necessary (R should take care of loading dependencies) but try installating data.table also. Platform: x86_64-apple-darwin17.0 (64-bit) Choose Yes. Language(R, Python, SQL) Is there anything I can do to speed it up? I tried installing DESeq2 using: but it run into a lot of errors (some missing packages for some dependency packages etc) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files. So, supposedly the issue is with Hmisc. I am running a new install of R (3.5.0) and RStudio (1.1.414). From the console install.packages ("rlang") should fix this. Remember to always click on the red Show me the content on this page notice when navigating these older versions. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Already on GitHub? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so MathJax reference. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Installing Hmisc as suggested above did not solve the issue. Not the answer you're looking for? [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: DESeq2 installation in R - Bioconductor Why is there a voltage on my HDMI and coaxial cables? .onLoad failed in loadNamespace() for 'rlang', details: library(DESeq2) there is no package called Hmisc. And finally, install the problem packages, perhaps also DESeq2. After 3-4 manual installs everything worked. Warning: restored xfun, The downloaded binary packages are in Erasmus+ funds available! Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Bioconductor release. Running. I even tried BiocManager::install("XML") but all failed as shown below. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Not the answer you're looking for? I also tried something I found on google: but the installation had errors too, I can write them here if needed. Citation (from within R, I guess that means we can finally close this issue. If you preorder a special airline meal (e.g. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: I need help installing a package "DESeq2" having - RStudio Community How do you ensure that a red herring doesn't violate Chekhov's gun? install.packages ("zip") to your account. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Is a PhD visitor considered as a visiting scholar? Browse other questions tagged, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. ERROR: lazy loading failed for package Hmisc