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. 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. Good to know @hadley Thanks for reaching back so quick! For example, I needed to install 7 packages(Sejong, hash, rJava, tau, RSQLite, devtools, stringr) to install KoNLP package. It's incredible but my solution was to restart R and try again. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. --N To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 11. Policy. What can I do to resolve the issue? Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. rev2023.3.3.43278. hello, thanks for helping! Equivalently for Bioconductor packages, you may need to update your Bioconductor installation. "After the incident", I started to be more careful not to trip over things. may need compilation of C/C++/Fortran: rlang That's a bug I reported already a few times, but I don't know if it's sorted already. 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. Ask Ubuntu is a question and answer site for Ubuntu users and developers. (as lib is unspecified) Linear regulator thermal information missing in datasheet. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. The main problem of that was that I couldnt install RCurl. You can select a different mirror with chooseCRANmirror () and try the installation again. Relation between transaction data and transaction id. This worked for me in R 4.2.1 on Windows. 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: Is the bigvis package for R not available for R version 3.0.1? The packages include: broom, tidyr, tidyselect, vctrs, and rlang. Teams. 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. Linear regulator thermal information missing in datasheet, Find the package you want to install with, Determine which version you want to install. Is there a single-word adjective for "having exceptionally strong moral principles"? Are there tables of wastage rates for different fruit and veg? See also these questions referring to specific instances of this problem: My package doesn't work for R 2.15.2 install('DESeq2', lib = '/home/kostas/R/x86_64-pc-linux-gnu-library/3.6') It is common to be confused about the difference between a package and a library, or a package and a dataset. At first I had about 10 errors regarding packages I couldnt install. One thing that happened for me is that the version of R provided by my linux distribution (R version 3.0.2 provided by Ubuntu 14.04) was too old for the latest version of the package available on CRAN (in my case, plyr version 1.8.3 as of today). In a case like this, the alternative to upgrading the R installation is the solution already mentioned. Ubuntu and the circle of friends logo are trade marks of Canonical Limited and are used under licence. For problems with Ubuntu, check the README: This solution worked for me for debian for the package, When I try install.packages('foobarbaz', repos=NULL) I get error " Error in install.packages("pair", repos = NULL) : type == "both" cannot be used with 'repos = NULL'", Thanks for the comment - I think I forgot to write the, This way do solved my problem, but still update my R to the newest version(from. Connect and share knowledge within a single location that is structured and easy to search. 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. What is the purpose of non-series Shimano components? There is a package TSA from CRAN. Post questions about Bioconductor Linear regulator thermal information missing in datasheet. 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)". Done Building dependency tree Reading state information. How would "dark matter", subject only to gravity, behave? You signed in with another tab or window. to your account. https://travis-ci.org/github/ramiromagno/gwasrapidd/jobs/740002831. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? package "makeR" is not available (for version 3.0.2) Can carbocations exist in a nonpolar solvent? package 'Rbbg' is not available (for R version 2.15.2) (As with installr, you may need to install.packages("remotes") first. How to handle a hobby that makes income in US. If so, how close was it? If pkg-config. Install from local (i.e. 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. The package is not in the repositories you selected. Bulk update symbol size units from mm to map units in rule-based symbology. There seems to be a problem with some versions of R and libcurl. 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. @bli you're right, I stand corrected. To view documentation for the version of this package installed To learn more, see our tips on writing great answers. 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. ), 9. If you are behind a proxy server check the configuration using Sys.getenv("http_proxy") within R. when I try to install the package , it returns a message like this: Warning message: Is the God of a monotheism necessarily omnipotent? This should fix the issue. pinky1 March 21, 2021, 1:20am #3 Linux installing from either CRAN or GitHub. I had the same problem (on Linux) which could be solved changing the proxy settings. What is the point of Thrower's Bandolier? In the R 3.2.3 (new in 2016) there was a bug, preventing it some times from finding correct package. In .inet_warning(msg) : 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. For context, this afternoon I had version 5.2.1, received similar errors and decided to upgrade. Thanks @zkamvar, I have homebrew and that worked for freetype. 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. The main problem of that was that I couldnt install RCurl. Identify those arcade games from a 1983 Brazilian music video, Trying to understand how to get this basic Fourier Series. Local regression, likelihood and density estimation methods as described in the 1999 book by Loader. Is the plyr package for R not available for R version 3.0.2? In this case the error message is slightly misleading: package 'foobarbaz' is not available (for R version x.y.z). rev2023.3.3.43278. It only takes a minute to sign up. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that . (Of course, you may need to install.packages("installr") first.). How to use Slater Type Orbitals as a basis functions in matrix method correctly? guide. package twitterR is not available (for R version 3.1.0) Please what could be a reason for this error? BEGIN To permanently change this, add a line like setRepositories(ind = c(1:6, 8)) to your Rprofile.site file. In RStudio, go to the "Packages" tab and remove all the packages (click on the x) raising the "red-flags" in the required updates. Such a relief reading it now! 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 Configuration failed to find the --static freetype2 library. package ggbiplot is not available (for R version 3.5.3)? limit n,mnm - the incident has nothing to do with me; can I use this this way? Why doesn't R think that the package is available? Restart RStudio and then re-install the main package allowing for it to run through the updates on the dependencies. But it still does not work. Already on GitHub? Why did Ukraine abstain from the UNHRC vote on China? So, maybe try updating your operating system? 'getOption("repos")' replaces Bioconductor standard repositories, see Differential expression analysis of RNA-seq expression profiles with biological replication. Already on GitHub? 3. For some reason, the package was still there, but install.packages was only looking at the updated (and incompatible) version. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Follow Up: struct sockaddr storage initialization by network format-string. My solution is to read the output of dependent packages that are listed in red and identified with issues (e.g., "cannot install"). 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. Find centralized, trusted content and collaborate around the technologies you use most. Recovering from a blunder I made while emailing a professor, How to tell which packages are held back due to phased updates. 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. There are several reasons why a package may not be available. Package fribidi was not found in the pkg-config search path. package RTN is not available (for R version 3.0.1) Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Asking for help, clarification, or responding to other answers. A concrete example: the latest CRAN version of package rattle for data mining, 5.3.0, does not support R version 3.4 because it had a big update between package versions 5.2.0 (R >= 2.13.0) and 5.3.0 (R >=3.5). Asking for help, clarification, or responding to other answers. That's only for bioconductor packages, and this is also the way bioconductor packages have to be installed. dependency Cairo is not available for package ComplexHeatmap on Ubuntu 20.04 LTS, How Intuit democratizes AI development across teams through reusability. 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. Why do many companies reject expired SSL certificates as bugs in bug bounties? I've just updated R to version 3.6.2 "dark and stormy night" released December 12th last year. Is there a single-word adjective for "having exceptionally strong moral principles"? R. If you want to install it: install.packages ("TSA") If you already have .tar.gz files. Unfortunately, it seems that I'd have to replicate the process for other packages with non-zero status as well: I wonder if these interdependencies can be resolved within R? For the Nozomi from Shinagawa to Osaka, say on a Saturday afternoon, would tickets/seats typically be available - or would you need to book? 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 . Another possible warnings message you may get when interacting with CRAN mirrors is: Warning: unable to access index for repository Which may indicate the selected CRAN repository is currently be unavailable. R (or another dependency) is out of date and you don't want to update it. 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. 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. 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. 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. Suspected that this was the case. . In many cases are just mirrors out of date. Author: Yunshun Chen, Aaron TL Lun, Davis J McCarthy, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth, Maintainer: Yunshun Chen
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