hello, thanks for helping! That was meant to control the source of packages for layman users, but as a developer, you can in most cases change that by: If you know what you are doing and may need more than one package that might not be available in your system's CRAN, you can set this up in your project .Rprofile. This function can install multiple packages with their dependencies using https://cran.rstudio.com/: This is what I finally could do for installing psych package in R-3.4.1 when I got the same warning, 2:downloaded it manually having tar.gz extension, 3:Chose the option "Package Archive File (.zip;.tar.gz)" for install packages in R, 4:browsed locally to the place where it was downloaded and clicked install. Did this satellite streak past the Hubble Space Telescope so close that it was out of focus? Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. The main problem of that was that I couldnt install RCurl. Turns out, the CRAN snapshot they have on the HPC is from Jan. 2018 (almost 2 years old) and indeed pkgdown did not exist then. In the R 3.2.3 (new in 2016) there was a bug, preventing it some times from finding correct package. Recovering from a blunder I made while emailing a professor. Differential expression analysis of RNA-seq expression profiles with biological replication. In my ~/.Renviron I had the following lines (from https://support.rstudio.com/hc/en-us/articles/200488488-Configuring-R-to-Use-an-HTTP-or-HTTPS-Proxy) causing the problem: solved the problem. rev2023.3.3.43278. To see which repositories R will look in for your package, and optionally select some additional ones. Sometimes the package maintainer may show R version gaps that it does not support. I suggest using Hadley Wickham's devtools package. You can turn off this check by setting. "After the incident", I started to be more careful not to trip over things. Sign in To subscribe to this RSS feed, copy and paste this URL into your RSS reader. How can I use it? This helped me installing a package on a server (i.e. set n=N-1; Typically the lines above "non-zero exit status" indicate what has gone wrong. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that . Full text of the 'Sri Mahalakshmi Dhyanam & Stotram', Relation between transaction data and transaction id. Is the plyr package for R not available for R version 3.0.2? Assuming that it is reasonably compliant with CRAN standards, you can still download it using install.packages; you just have to specify the repository URL. In a case like this, the alternative to upgrading the R installation is the solution already mentioned. In my case the solution was to simply upgrade R. I found a slight variation on #6 package is out of date from the excellent solution by @Richie Cotton. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? R. Documentation: Reference manual: locfit.pdf Downloads: Reverse dependencies: Linking: Please use the canonical form https://CRAN.R-project.org/package=locfitto link to this page. C, C++, FORTRAN) then on Windows install Rtools or on OS X install the developer tools accompanying XCode, and install the source version of the package via: On CRAN, you can tell if you'll need special tools to build the package from source by looking at the NeedsCompilation flag in the description. Use of this site constitutes acceptance of our User Agreement and Privacy # Write you. Warning message: package (s) not installed when version (s) same as current; use `force = TRUE` to re-install: 'limma' Please help and let me know to find solution. Author Anirban166 on Oct 29, 2020 edited Thanks @zkamvar, I have homebrew and that worked for freetype. Equivalently for Bioconductor packages, you may need to update your Bioconductor installation. with https://packagemanager.rstudio.com/client/#/. 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. Package bigmemory not installing on R 64 3.0.2 Thanks a lot Mensur Dlakic ! Will Gnome 43 be included in the upgrades of 22.04 Jammy? Thats whats the obvious and what got through my mind at first but taking under consideration that I just got into the field I thought that this is no way whats going on and that it has to do with some deeper R knowledge. The R version is not the issue - I have all of those packages installed under 3.6.2. Maybe I could have tried to update R using updateR(), but I'm afraid that doing so would interfere with my distribution's package manager. What OS & release are you using? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. You'll need to provide more details from the error message. To permanently change this, add a line like setRepositories(ind = c(1:6, 8)) to your Rprofile.site file. If you are into extreme makeovers, upgrading your R to the latest version could work as well. An alternative is to install from the GitHub CRAN mirror. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? install('DESeq2', lib = '/home/kostas/R/x86_64-pc-linux-gnu-library/3.6') What is the purpose of non-series Shimano components? The package is not in the repositories you selected. Why do many companies reject expired SSL certificates as bugs in bug bounties? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. package is not available (for R version 2.15.2) DESeq2 installation Error (ERROR: dependency 'locfit' is not available for package 'DESeq2') 0 tsomakiank 0 @93aec3aa Last seen 9 months ago Greece Hello everybody! same issue today with renv::install("pkgdown") and install.packages("pkgdown") persisted after conda install -c anaconda fribidi. package RTN is not available (for R version 3.0.1) There seems to be a problem with some versions of R and libcurl. install.packages("rlang") Why is there a voltage on my HDMI and coaxial cables? Is there a single-word adjective for "having exceptionally strong moral principles"? So, maybe try updating your operating system? . Otherwise, you will need to set up Rtools in order to install from source. locfit: Local Regression, Likelihood and Density Estimation Local regression, likelihood and density estimation methods as described in the 1999 book by Loader. EconomiCurtis closed This topic has been closed. How to install 'Rcpp, package? How to import local packages without gopath. rev2023.3.3.43278. Please read the posting Why do small African island nations perform better than African continental nations, considering democracy and human development? OOOh really! If pkg-config. Already on GitHub? At the very least, you will usually want CRAN to be selected, and CRAN (extras) if you use Windows, and the Bioc* repositories if you do any biological analyses. 3. Any other solutions? By clicking Sign up for GitHub, you agree to our terms of service and Same here. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE. This worked for me in R 4.2.1 on Windows. How to fix this error in R while installing packages? apt or yum). Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Install the package devtools if you don't have it (it includes package remotes) and then install the specific version that will work in your current R. You can look up that information on the CRAN page for the specific package archives. I just tested and I don't need to set the repository if I just launch R from the terminal--only from within r-studio. Perhaps you should add the directory containing `fribidi.pc. DEseq2edgeR R , Cannot find xml2-config ERROR: configuration failed for package XML , xml, ERROR: dependency RCurl is not available for package GenomeInfoDb, RCurl, ERROR: dependency locfit is not available for package DESeq2 locfit1.5-9.2, sudo conda , Rpackage xx is not available (for R version xx), internal server error_Rdependencies * are not available for package, #ubuntu centosyum, 'https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.2.tar.gz', RNA, 2016A survey of best practices for RNA-seq data analysisRNATopHat,STARBowtie.TopHatHISAT1. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. rev2023.3.3.43278. For R 3.6.3 you'll need Bioconductor 3.10: if (!requireNamespace ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install (version = "3.10") Then you install DESeq2: What is the point of Thrower's Bandolier? as described in this SO answer by imanuelc and the Details section of ?install.packages. How do I align things in the following tabular environment? may need compilation of C/C++/Fortran: rlang data.table vs dplyr: can one do something well the other can't or does poorly? It almost always works for me when I use bioconductor as source and then invoke biocLite. In this case the error message is slightly misleading: package 'foobarbaz' is not available (for R version x.y.z). In RStudio, go to the "Packages" tab and remove all the packages (click on the x) raising the "red-flags" in the required updates. Ask Ubuntu is a question and answer site for Ubuntu users and developers. I run into this error ("package XXX is not available for R version X.X.X") when trying to install pkgdown in my RStudio on my company's HPC. The solution was to find the URL of the compatible version and force install.packages to use it, as follows: This saved me a lot of time debugging what's wrong. Is there a chance the problem is on my end, mac OSX Catalina? Ideally, you would update your R installation to the latest version (3.4.3). Using Kolmogorov complexity to measure difficulty of problems? - the incident has nothing to do with me; can I use this this way? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. In RStudio, go to the "Packages" tab and remove all the packages (click on the x) raising the "red-flags" in the required updates. It allows loading package from given directory: Thanks for contributing an answer to Stack Overflow! The first thing to test is have you spelled the name of the package correctly? I have had the same problem on Mac (R version 3.2.2) and Ubuntu (R version 3.0.2) and in both instances it was resolved simply by running this before the install.packages command. How to view hierarchical package structure in Eclipse package explorer, How to unload a package without restarting R. How to find out which package version is loaded in R? If you want to install it: If you already have .tar.gz files. @laresbernardo this will resolve itself in 24-48 hours when the macOS binary of textshaping is available. rev2023.3.3.43278. pinky1: ERROR: dependency 'locfit' is not available for package 'TSA' The locfit package (which is a package dependency) requires R >= 3.5 and since you are using an even older R version, you would have to update R to be able to install it. Citation (from within R, For example, I needed to install 7 packages(Sejong, hash, rJava, tau, RSQLite, devtools, stringr) to install KoNLP package. Hi, I would like to install the package DESeq2, however it doesnt look to work with the last version of R. > install.packages("DESeq2") Warning in install.packages : DESeq2 installation Error (ERROR: dependency locfit is not available for package DESeq2), Traffic: 822 users visited in the last hour, https://cran.r-project.org/src/contrib/Archive/locfit/, User Agreement and Privacy ), 9. You can select a different mirror with chooseCRANmirror() and try the installation again. Here's how to install it via apt for ubuntu: The easiest way to resolve this problem is to install a binary, e.g. Thank you for attention I'm running a RNA-seq analysis so tried to install differents pkgs. https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, https://stackoverflow.com/questions/1474081/how-do-i-install-an-r-package-from-source. Identify those arcade games from a 1983 Brazilian music video, Trying to understand how to get this basic Fourier Series. is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: -------------------------- [ERROR MESSAGE] ---------------------------, --------------------------------------------------------------------, ERROR: configuration failed for package systemfonts, * removing /usr/local/lib/R/4.0/site-library/systemfonts, installation of package systemfonts had non-zero exit status, ERROR: dependency systemfonts is not available for package textshaping, * removing /usr/local/lib/R/4.0/site-library/textshaping, installation of package textshaping had non-zero exit status, ERROR: dependencies systemfonts, textshaping are not available for package ragg, * removing /usr/local/lib/R/4.0/site-library/ragg, installation of package ragg had non-zero exit status, ERROR: dependency ragg is not available for package pkgdown, * removing /usr/local/lib/R/4.0/site-library/pkgdown, installation of package pkgdown had non-zero exit status, (converted from warning) installation of package systemfonts had non-zero exit status. Hello everybody! See also Names of R's available packages, ?available.packages. My solution is to read the output of dependent packages that are listed in red and identified with issues (e.g., "cannot install"). In some cases, you need to install several packages in advance to use the package you want to use. Not the answer you're looking for? see the ideas at You signed in with another tab or window. privacy statement. Edit (04/08/2020): I recently had an issue with a package (XML) reportedly not available for my R version (3.6.3, latest supported on Debian stretch), after an update of the package in CRAN. The package is on GitHub/Bitbucket/Gitorious. 8. Your package is in a non-standard repository (e.g. See also these questions referring to specific instances of this problem: My package doesn't work for R 2.15.2 Why doesn't R think that the package is available? Please what could be a reason for this error? package in your R session. Why do small African island nations perform better than African continental nations, considering democracy and human development? Configuration failed to find the --static freetype2 library. I know that may sound ridiculous given that your R version is only a couple of years old, but I don't make the rules. Why did Ukraine abstain from the UNHRC vote on China? How to fix "Attempted relative import in non-package" even with __init__.py, Install package from source throws "package not available" in R, package slidify not available as a binary package for R version 3.1.3, package gplots is not available for R version 3.0.2, warning: package grid is not available (for R version 3.1.2), not able to install fable package (error: is not available (for R version 3.4.2). Dependency Rglpk is not available for package fPortfolio '?repositories' for details. ), same here: when I try to install the package , it returns a message like this: Warning message: when I try to install the package , it returns a message like this: Warning message: In .inet_warning(msg) : package 'ImpulseDE2' is not available for Bioconductor version '3.14' A version of this package for y. ERROR: dependency 'locfit' is not available for package 'DESeq2' locfit1.5-9.2 #R install.packages('https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.2.tar.gz',repos = NULL) 1 2 DEseq2edgeR In .inet_warning(msg) : To subscribe to this RSS feed, copy and paste this URL into your RSS reader. That's a bug I reported already a few times, but I don't know if it's sorted already. hello, thanks for helping! Here's more info from the error as requested: Edit 2: An exhaustive printout of all errors and messages as requested in comments: When you call install.packages("broom") (or insert package), it appears the message you receive is: Do you want to install from sources the packages which need compilation? Using Kolmogorov complexity to measure difficulty of problems? Sign in https://travis-ci.org/github/ramiromagno/gwasrapidd/jobs/740002831. Thanks @zkamvar, I have homebrew and that worked for freetype. These packages require the remotes package to install. For the Nozomi from Shinagawa to Osaka, say on a Saturday afternoon, would tickets/seats typically be available - or would you need to book? Asking for help, clarification, or responding to other answers. Relation between transaction data and transaction id. How would "dark matter", subject only to gravity, behave? Uninstall the oldest one, then try your package installation again! package ImpulseDE2 is not available for Bioconductor version '3.14', A version of this package for your version of R might be available elsewhere, By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. What to do when a package is not available for our R version? I am trying to install DESeq2 and I keep getting errors. Is the bigvis package for R not available for R version 3.0.1? The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup. Warning: cannot remove prior installation of package 'scales' The downloaded binary packages are in C:\Users\admin\AppData\Local\Temp\RtmpQXIjyl\downloaded_packages package syncwave/mvcwt is not available (for R version 3.0.2) Additionally, some packages are available only via the sources for some or all platforms. For the Nozomi from Shinagawa to Osaka, say on a Saturday afternoon, would tickets/seats typically be available - or would you need to book? --N Installing package into C:/Users/dimarcantonio/Documents/R/win-library/3.2 What happens if you use install.packages("rlang")? I've tried installing the following packages but have received the same error, "installation of package X had non-zero exit status". You can select a different mirror with chooseCRANmirror () and try the installation again. limit n offset m mm limit n,mnm Package which is only available in source form, and The problem was not the version of R, it was the repos parameter. There are several reasons why a package may not be available. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Equation alignment in aligned environment not working properly. From searching I managed to install RCurl but I still get the bellow error. Making statements based on opinion; back them up with references or personal experience. I fixed this error on Ubuntu by carefully following the instructions for installing R. This included: For step 1 you can chose any CRAN download mirror in place of my University of Toronto one if you would like. It only takes a minute to sign up. Find centralized, trusted content and collaborate around the technologies you use most. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy.