Powered by Discourse, best viewed with JavaScript enabled, Problems with tidyverse load - Error: package or namespace load failed for tidyverse in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace scales 0.4.0 is already loaded, but >= 0.4.1 is required, ERROR: dependency rlang is not available for package dbplyr - R 3.4.3, removing 'C:/Users/dimarcantonio/Documents/R/win-library/3.2/dbplyr', removing 'C:/Users/dimarcantonio/Documents/R/win-library/3.2/hms', removing 'C:/Users/dimarcantonio/Documents/R/win-library/3.2/tidyverse'. So, maybe try updating your operating system? package 'Rbbg' is not available (for R version 2.15.2), package is not available (for R version 2.15.2), package doMC NOT available for R version 3.0.0 warning in install.packages, Dependency Rglpk is not available for package fPortfolio. Can I tell police to wait and call a lawyer when served with a search warrant? data.table vs dplyr: can one do something well the other can't or does poorly? Local regression, likelihood and density estimation methods as described in the 1999 book by Loader. 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 with https://packagemanager.rstudio.com/client/#/. Not the answer you're looking for? Package names are case sensitive in R. 2. to your account. I am trying to install DESeq2 and I keep getting errors. Look at. To view documentation for the version of this package installed 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. R (or another dependency) is out of date and you don't want to update it. Hello everybody! That error simply tells you that broom is not installed. package syncwave/mvcwt is not available (for R version 3.0.2), package diamonds is not available (for R version 3.0.0). The package is in a non-standard repository. 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. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that . - the incident has nothing to do with me; can I use this this way? The first thing to test is have you spelled the name of the package correctly? I've just updated R to version 3.6.2 "dark and stormy night" released December 12th last year. ERROR: dependency 'rlang' is not available for package 'dbplyr'. Find centralized, trusted content and collaborate around the technologies you use most. Using Kolmogorov complexity to measure difficulty of problems? Connect and share knowledge within a single location that is structured and easy to search. How to find out which package version is loaded in R? package ggbiplot is not available (for R version 3.5.3)? Here's how to install it via apt for ubuntu: The easiest way to resolve this problem is to install a binary, e.g. 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. Policy. I have tried to install Cairo using the command sudo apt-get install libcairo2-dev but I still get the same error. There is a package TSA from CRAN. Why does it seem like I am losing IP addresses after subnetting with the subnet mask of 255.255.255.192/26? "package rhipe is not available (for R version 3.1.2)". A package is a standardized collection of material extending R, e.g. Is the plyr package for R not available for R version 3.0.2? Try installing: * deb: libfontconfig1-dev (Debian, Ubuntu, etc), If --static freetype2 is already installed, check that, PATH and PKG_CONFIG_PATH contains a --static freetype2.pc file. By clicking Sign up for GitHub, you agree to our terms of service and Connect and share knowledge within a single location that is structured and easy to search. OOOh really! You can turn off this check by setting. 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). Making statements based on opinion; back them up with references or personal experience. If so, how close was it? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. OOOh really! 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. To permanently change this, add a line like setRepositories(ind = c(1:6, 8)) to your Rprofile.site file. Try no and compare results. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Is the God of a monotheism necessarily omnipotent? 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. install.packages("rlang") I am trying to install DESeq2 and I keep getting errors. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? 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. see the ideas at 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. That's a bug I reported already a few times, but I don't know if it's sorted already. set n=N-1; What is the point of Thrower's Bandolier? RHIPE on the other hand isn't in a CRAN-like repository and has its own installation instructions. If you want to install it: install.packages ("TSA") If you already have .tar.gz files. Why did Ukraine abstain from the UNHRC vote on China? It's incredible but my solution was to restart R and try again. Thanks @zkamvar, I have homebrew and that worked for freetype. install('DESeq2', lib = '/home/kostas/R/x86_64-pc-linux-gnu-library/3.6') apt or yum). Asking for help, clarification, or responding to other answers. in your system, start R and enter: Follow How do I align things in the following tabular environment? 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. Thanks for contributing an answer to Stack Overflow! Relation between transaction data and transaction id. Have a question about this project? I did install.packages('path/to/source/code/of/foobarbaz', type='source', repos=NULL) which worked for me in this occasion. try this install_github("YosefLab/ImpulseDE2"). What can I do to resolve the issue? Note that when using RStudio, you get this warning as well when installing from another repo than CRAN. In many cases are just mirrors out of date. Why doesn't R think that the package is available? You are using an older R version (3.6.3) for which not all packages are available. Please what could be a reason for this error? Learn more about Teams Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Recovering from a blunder I made while emailing a professor, How to tell which packages are held back due to phased updates. Done Building dependency tree Reading state information. What is the purpose of non-series Shimano components? That shouldn't be necessary, but the error message could narrow down the possibilities. Sometimes the package maintainer may show R version gaps that it does not support. R. locfit: Local Regression, Likelihood and Density Estimation. To see which repositories R will look in for your package, and optionally select some additional ones. thank you Limma Packaging. Is the bigvis package for R not available for R version 3.0.1? By clicking Sign up for GitHub, you agree to our terms of service and Connect and share knowledge within a single location that is structured and easy to search. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. limit (Of course, you may need to install.packages("installr") first.). To learn more, see our tips on writing great answers. You can do the same for https. The code in, @bli it doesn't guarantee compatibility, it updates everything to the latest version (unless you put. 2 Answers Sorted by: 1 Bioconductor is a package management tool for R that allows you to install the appropriate package versions for your R version. It is common to be confused about the difference between a package and a library, or a package and a dataset. Configuration failed to find the --static freetype2 library. same issue today with renv::install("pkgdown") and install.packages("pkgdown") persisted after conda install -c anaconda fribidi. Install from local (i.e. Connect and share knowledge within a single location that is structured and easy to search. I can not seem to figure out how to install the package in R. I have tried the codes you suggested: https://stackoverflow.com/questions/1474081/how-do-i-install-an-r-package-from-source. @Tmacphee13 @joycekang, installing on Linux, you need to install libharfbuzz using your Linux package distribution manager (e.g. 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 The best answers are voted up and rise to the top, Not the answer you're looking for? dependency Cairo is not available for package ComplexHeatmap on Ubuntu 20.04 LTS, How Intuit democratizes AI development across teams through reusability. The error message from {systemfonts} suggests that you need to install the freetype2 library on your machine: If you don't have homebrew, I would suggest to install it ( https://brew.sh/) and then run brew install freetype from your terminal. @bli you're right, I stand corrected. Restart RStudio and then re-install the main package allowing for it to run through the updates on the dependencies. rev2023.3.3.43278. The solution was suggested by a friend, however, I haven't been able to find it in any of the forums, hence submitting this answer for others. If the package requires compiling code (e.g. I got "package is not available", package dataset is not available (for R version 3.1.1), "package rhipe is not available (for R version 3.1.2)", https://cran.r-project.org/src/contrib/Archive/, cran.r-project.org/bin/linux/ubuntu/README, https://support.rstudio.com/hc/en-us/articles/200488488-Configuring-R-to-Use-an-HTTP-or-HTTPS-Proxy, How Intuit democratizes AI development across teams through reusability. Well occasionally send you account related emails. Same here. If you want to install it: If you already have .tar.gz files. Well occasionally send you account related emails. I've tried installing the following packages but have received the same error, "installation of package X had non-zero exit status". AC Op-amp integrator with DC Gain Control in LTspice, Radial axis transformation in polar kernel density estimate, Trying to understand how to get this basic Fourier Series, Difficulties with estimation of epsilon-delta limit proof. ==================================================, to the PKG_CONFIG_PATH environment variable, --------------------------- [ANTICONF] --------------------------------. Ideally, you would update your R installation to the latest version (3.4.3). RETURN ( Use of this site constitutes acceptance of our User Agreement and Privacy ), same here: 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. To learn more, see our tips on writing great answers. At first I had about 10 errors regarding packages I couldnt install. At first I had about 10 errors regarding packages I couldnt install. providing code, data, or documentation. limit n offset m mm Disconnect between goals and daily tasksIs it me, or the industry? 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. Below are the commands I have run and the respective outputs: To verify the proper installation of Cairo: You are probably do not want to read the messages which are shown during compilation. Ubuntu and the circle of friends logo are trade marks of Canonical Limited and are used under licence. It only takes a minute to sign up. In some cases, you need to install several packages in advance to use the package you want to use. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Asking for help, clarification, or responding to other answers. installation of package had non-zero exit status, How Intuit democratizes AI development across teams through reusability. Browse other questions tagged. For some reason, the package was still there, but install.packages was only looking at the updated (and incompatible) version. package ImpulseDE2 is not available for Bioconductor version '3.14', A version of this package for your version of R might be available elsewhere, Hisat21.1 , SQLlimitoffset guide. Cloning the repository woudnt do it either. package in your R session. slidify package not available in R 3.1.2? Warning this is not exactly best practice. not via RStudio). You may get a warning: dependencies 'xyz' not available for the package ,then first install those from the repository and then do steps 3-4 Since this is a large matrix, you may wish to use the data viewer to examine it. Ask Ubuntu is a question and answer site for Ubuntu users and developers. Policy. pinky1 March 21, 2021, 1:20am #3 Does this help you https://stackoverflow.com/questions/1474081/how-do-i-install-an-r-package-from-source? Seeing same as @joycekang. If so, how close was it? https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. Did this satellite streak past the Hubble Space Telescope so close that it was out of focus? --> install_logs_.md. Why do small African island nations perform better than African continental nations, considering democracy and human development? Making statements based on opinion; back them up with references or personal experience. Any other solutions? If it's just one package, maybe just use install.packages("package name", repos = "a newer CRAN than your company's archaic CRAN snapshot"). ERROR installing EnhancedVolcano in R4.1. 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. Recovering from a blunder I made while emailing a professor. Policy. Usually stated dependency on R version is there for a reason, it may be wise to check what such change will potentially break. For context, this afternoon I had version 5.2.1, received similar errors and decided to upgrade. Equation alignment in aligned environment not working properly, Styling contours by colour and by line thickness in QGIS. I got "package is not available" Otherwise, you will need to set up Rtools in order to install from source. Author Anirban166 on Oct 29, 2020 edited Thanks @zkamvar, I have homebrew and that worked for freetype. I have ran into this issue with other packages. The packages include: broom, tidyr, tidyselect, vctrs, and rlang. That did the trick! package dataset is not available (for R version 3.1.1) You didn't look in the right repository, Next, you should check to see if the package is available. 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. Alternatively, you can quickly check to see if the package is available by testing against the row names. Disconnect between goals and daily tasksIs it me, or the industry? 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. To verify the proper installation of Cairo: package "makeR" is not available (for version 3.0.2) To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. I changed the Action file to run install.packages("pkgdown") instead of remotes::install_dev("pkgdown") as I needed the site to be updated today. What to do when a package is not available for our R version? DESeq2 installation Error (ERROR: dependency 'locfit' is not available for package 'DESeq2') 0 tsomakiank 0 @93aec3aa Last seen 9 months ago Greece Hello everybody! Use Bioc installation steps: https://bioconductor.org/install. Linear regulator thermal information missing in datasheet. Dependency Rglpk is not available for package fPortfolio 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? In .inet_warning(msg) : Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. The problem was not the version of R, it was the repos parameter. . Is it possible to rotate a window 90 degrees if it has the same length and width? In the R 3.2.3 (new in 2016) there was a bug, preventing it some times from finding correct package. 10. (As with installr, you may need to install.packages("remotes") first. It allows loading package from given directory: Thanks for contributing an answer to Stack Overflow! Please clarify. Warning message: package 'GenomeInfoDbData' is not available (as a binary package for R version 4.0.2) price793 November 24, 2020, 9:43pm #6 Hi Tulip, I figured out the problem. 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. You'll need to provide more details from the error message. @JorisMeys It seems to me that all packages I tried to install so far were available via this method, but I'm mainly using R for bioinformatics.