warning dependency locfit is not available

It may have been archived (if it is no longer maintained and no longer passes R CMD check tests). (Fresh Ubuntu 20.04 LTS Setup). BEGIN Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? What to do when a package is not available for our R version? Why does Mister Mxyzptlk need to have a weakness in the comics? Can carbocations exist in a nonpolar solvent? In the R 3.2.3 (new in 2016) there was a bug, preventing it some times from finding correct package. Otherwise, you can use pak::pkg_system_requirements() to get an up-to-date list of system deps. Making statements based on opinion; back them up with references or personal experience. @laresbernardo this will resolve itself in 24-48 hours when the macOS binary of textshaping is available. I tried to install pkgdown via devtools fresh on a new OS X (Catalina) machine, but the installation seems to fail (non-zero exit status) with error implications for packages such as freetype2 and systemfonts, even with dependencies set: The text was updated successfully, but these errors were encountered: 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. It allows loading package from given directory: 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. Did this satellite streak past the Hubble Space Telescope so close that it was out of focus? 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. installation - How should I deal with "package 'xxx' is not available How do I align things in the following tabular environment? Why do small African island nations perform better than African continental nations, considering democracy and human development? package diamonds is not available (for R version 3.0.0) "After the incident", I started to be more careful not to trip over things. Not the answer you're looking for? How do I align things in the following tabular environment? Identify those arcade games from a 1983 Brazilian music video, Trying to understand how to get this basic Fourier Series. There are several reasons why a package may not be available. Note that when using RStudio, you get this warning as well when installing from another repo than CRAN. guide. Hisat21.1 , SQLlimitoffset @bli you're right, I stand corrected. Already on GitHub? Linear regulator thermal information missing in datasheet, Find the package you want to install with, Determine which version you want to install. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Unable to install packages in latest version of RStudio and R Version.3.1.1, package pbkrtest is not available (for R version 3.2.2), R packages rgdal / rgeos "is not available (for R version 3.1.1)". If you are into extreme makeovers, upgrading your R to the latest version could work as well. locfit: Local Regression, Likelihood and Density Estimation. --N OOOh really! 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. Try no and compare results. Is there a single-word adjective for "having exceptionally strong moral principles"? Use of this site constitutes acceptance of our User Agreement and Privacy ERROR installing EnhancedVolcano in R4.1. Learn more about Stack Overflow the company, and our products. A library is a place (directory) where R knows to find packages it can use, It may have a dependency on a more recent version of R (or one of the packages that it imports/depends upon does). R (or another dependency) is out of date and you don't want to update it. Warning: cannot remove prior installation of package 'scales' The downloaded binary packages are in C:\Users\admin\AppData\Local\Temp\RtmpQXIjyl\downloaded_packages 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 to your account. Will Gnome 43 be included in the upgrades of 22.04 Jammy? Bioconductor - edgeR My solution is to read the output of dependent packages that are listed in red and identified with issues (e.g., "cannot install"). What is the purpose of non-series Shimano components? Remove the offending line with your text editor e.g. 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. Installation failure or a non-zero exit status, https://travis-ci.org/github/ramiromagno/gwasrapidd/jobs/740002831, https://packagemanager.rstudio.com/client/#/, init--> Install Errors. @Anirban166 you appear to be compiling all these packages from source; you'll find life much easier if you instead install binaries. https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. --> install_logs_.md. You can turn off this check by setting. Asking for help, clarification, or responding to other answers. Another possible warnings message you may get when interacting with CRAN mirrors is: Which may indicate the selected CRAN repository is currently be unavailable. hello, thanks for helping! '?repositories' for details. 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. The first thing to test is have you spelled the name of the package correctly? package 'destiny' is not available for Bioconductor version '3.13 Ask Ubuntu is a question and answer site for Ubuntu users and developers. How to install 'Rcpp, package? How to install edgeR Bioconductor package in ubuntu 20.4..? - ResearchGate package DESeq2 installation with R. - Bioconductor These will not be installed. You didn't look in the right repository, Next, you should check to see if the package is available. Done Building dependency tree Reading state information. Equivalently for Bioconductor packages, you may need to update your Bioconductor installation. I got "package is not available" It would appear that either versions 1.5-9.2 or 1.5-9.4 will be compatible with your R version, so maybe installing one of those ahead of DESeq2 will do the trick. I did install.packages('path/to/source/code/of/foobarbaz', type='source', repos=NULL) which worked for me in this occasion. I had the same problem (on Linux) which could be solved changing the proxy settings. Trouble Installing geoR package thank you Limma Packaging. Linear regulator thermal information missing in datasheet. Installation instructions to use this 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'm having the same error when building my library's documentation with Github Actions (check here). How would "dark matter", subject only to gravity, behave? Bulk update symbol size units from mm to map units in rule-based symbology. Sign in R . Do you maybe have the code for me. Configuration failed to find the --static freetype2 library. Restart RStudio and then re-install the main package allowing for it to run through the updates on the dependencies. 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. 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. OOOh really! 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. (Yes/no/cancel) to which you have answered yes. rev2023.3.3.43278. try this install_github("YosefLab/ImpulseDE2"). (As with installr, you may need to install.packages("remotes") first. https://travis-ci.org/github/ramiromagno/gwasrapidd/jobs/740002831. It is common to be confused about the difference between a package and a library, or a package and a dataset. 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. package in your R session. So, maybe try updating your operating system? Ah, I get it now. Differential expression analysis of RNA-seq expression profiles with biological replication. Is the plyr package for R not available for R version 3.0.2? 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Please clarify. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? pinky1 March 21, 2021, 1:20am #3 Connect and share knowledge within a single location that is structured and easy to search. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. Follow Up: struct sockaddr storage initialization by network format-string. 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 almost always works for me when I use bioconductor as source and then invoke biocLite. I had the same issue. You mention 20.04 in the title, but then report your release as 14.04 via tag? 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. Connect and share knowledge within a single location that is structured and easy to search. Connect and share knowledge within a single location that is structured and easy to search. 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. 8. I have ran into this issue with other packages. @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. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Making statements based on opinion; back them up with references or personal experience. Find centralized, trusted content and collaborate around the technologies you use most. 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'. This worked for me in R 4.2.1 on Windows. If pkg-config. set n=N-1; 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? The problem was not the version of R, it was the repos parameter. 1 Answer Sorted by: 0 There is a package TSA from CRAN. I was using an out of date operating system for R and it wouldn't install DESeq2 which was my main objective. Policy. What is the point of Thrower's Bandolier? as described in this SO answer by imanuelc and the Details section of ?install.packages. From searching I managed to install RCurl but I still get the bellow error. - the incident has nothing to do with me; can I use this this way? Follow Up: struct sockaddr storage initialization by network format-string. Share Improve this answer Follow answered Nov 28, 2022 at 20:27 Mark Thompson 143 9 Add a comment package dataset is not available (for R version 3.1.1) privacy statement. DESeq2 installation Error (ERROR: dependency 'locfit' is not available package twitterR is not available (for R version 3.1.0) Typically the lines above "non-zero exit status" indicate what has gone wrong. EnhancedVolcano dependency proj4 failed to install in R 4.1 ```In .inet_warning (msg) : package 'proj4 ' is not available for Bioconductor version '3.13' # include your problematic code here with any corresponding output # please also include the results of running the following in an R session . 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. See also these questions referring to specific instances of this problem: My package doesn't work for R 2.15.2 beyond top level package error in relative import. Please what could be a reason for this error? when I try to install the package , it returns a message like this: Warning message: I've tried installing the following packages but have received the same error, "installation of package X had non-zero exit status". install.packages("rlang") If you are behind a proxy server check the configuration using Sys.getenv("http_proxy") within R. It seems that the latest locfit version requires R 4.1.0. Differential expression analysis of RNA-seq expression profiles with biological replication. package RTN is not available (for R version 3.0.1) For Ubuntu 20.04 LTS with R 4.1 use commands below to install needed build-dependencies: Thanks for contributing an answer to Ask Ubuntu! slidify package not available in R 3.1.2? You can select a different mirror with chooseCRANmirror () and try the installation again. Is there a chance the problem is on my end, mac OSX Catalina? 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.

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