I need help installing a package "DESeq2" having BiocManager issues I suggest using Hadley Wickham's devtoolspackage. If so, how close was it? Making statements based on opinion; back them up with references or personal experience. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Ideally, you would update your R installation to the latest version (3.4.3). Why does it seem like I am losing IP addresses after subnetting with the subnet mask of 255.255.255.192/26? OOOh really! 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. https://travis-ci.org/github/ramiromagno/gwasrapidd/jobs/740002831. 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. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? The solution was to use the packaging system of my distribution instead of trying to install from R (apt-get install r-cran-plyr got me version 1.8.1 of plyr). Linux installing from either CRAN or GitHub. Look at. What is the point of Thrower's Bandolier? How to find out which package version is loaded in R? 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. 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. I had the same problem (on Linux) which could be solved changing the proxy settings. In many cases are just mirrors out of date. How do I align things in the following tabular environment? enter citation("edgeR")): To install this package, start R (version 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. You can turn off this check by setting. --N @Tmacphee13 @joycekang, installing on Linux, you need to install libharfbuzz using your Linux package distribution manager (e.g. 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). 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 was using an out of date operating system for R and it wouldn't install DESeq2 which was my main objective. Perhaps you should add the directory containing `fribidi.pc. In this case, you can load an old version of the package using install_version(). Teams. 10. Find centralized, trusted content and collaborate around the technologies you use most. Otherwise, you will need to set up Rtools in order to install from source. Making statements based on opinion; back them up with references or personal experience. 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. You can do the same for https. DESeq2 installation Error (ERROR: dependency 'locfit' is not available for package 'DESeq2') 0 tsomakiank 0 @93aec3aa Last seen 9 months ago Greece Hello everybody! package in your R session. Is it possible to rotate a window 90 degrees if it has the same length and width? Have a question about this project? Install from local (i.e. EconomiCurtis closed This topic has been closed. @joycekang on which operating system are you installing pkgdown, and what version are you installing (CRAN or GitHub)? Equation alignment in aligned environment not working properly. rev2023.3.3.43278. ERROR installing EnhancedVolcano in R4.1 - Bioconductor By clicking Sign up for GitHub, you agree to our terms of service and I'm having the same error when building my library's documentation with Github Actions (check here). Bulk update symbol size units from mm to map units in rule-based symbology. (Of course, you may need to install.packages("installr") first.). 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. To learn more, see our tips on writing great answers. Done Building dependency tree Reading state information. Recovering from a blunder I made while emailing a professor. Learn more about Teams dependency 'Cairo' is not available for package 'ComplexHeatmap' on 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 , Gordon Smyth , Aaron Lun , Mark Robinson . Trouble Installing geoR package This helped me installing a package on a server (i.e. Linear regulator thermal information missing in datasheet. dependency Cairo is not available for package ComplexHeatmap on Ubuntu 20.04 LTS, How Intuit democratizes AI development across teams through reusability. Post questions about Bioconductor You signed in with another tab or window. Find centralized, trusted content and collaborate around the technologies you use most. The main problem of that was that I couldnt install RCurl. What is the purpose of non-series Shimano components? The R version is not the issue - I have all of those packages installed under 3.6.2. not via RStudio). "After the incident", I started to be more careful not to trip over things. 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. when I try to install the package , it returns a message like this: Warning message: Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Thanks for contributing an answer to Stack Overflow! If pkg-config. CREATE FUNCTION getNthHighestSalary(N INT) RETURNS INT What was going on here? Ubuntu and the circle of friends logo are trade marks of Canonical Limited and are used under licence. DEseq2edgeR_edger_-WTF-CSDN On Windows, this is most easily done via the installr package. Extending Mensur's answer, here are previous releases of locfit: https://cran.r-project.org/src/contrib/Archive/locfit/. I've examined documentation for broom and I didn't see anything saying that it explicitly is only supported by some previous version. OOOh really! If it's just one package, maybe just use install.packages("package name", repos = "a newer CRAN than your company's archaic CRAN snapshot"). Is there a single-word adjective for "having exceptionally strong moral principles"? - the incident has nothing to do with me; can I use this this way? 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? Bioconductor - edgeR rev2023.3.3.43278. what is wrong and how should I handle it ? The Cairo package also requires X11/Intrinsic.h from libxt-dev package. Policy. How to use Slater Type Orbitals as a basis functions in matrix method correctly? @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. 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 How to handle a hobby that makes income in US. 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. 'getOption("repos")' replaces Bioconductor standard repositories, see 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. package 'Rbbg' is not available (for R version 2.15.2) r - installation of package had non-zero exit status - Stack Overflow Suspected that this was the case. See also Names of R's available packages, ?available.packages. DESeq2 installation Error (ERROR: dependency 'locfit' is not available If you are behind a proxy server check the configuration using Sys.getenv("http_proxy") within R. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. Asking for help, clarification, or responding to other answers. 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. For example, I needed to install 7 packages(Sejong, hash, rJava, tau, RSQLite, devtools, stringr) to install KoNLP package. locfit: Local Regression, Likelihood and Density Estimation. Making statements based on opinion; back them up with references or personal experience. package is not available (for R version 2.15.2) Did this satellite streak past the Hubble Space Telescope so close that it was out of focus? ), 9. 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. 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 : My solution is to read the output of dependent packages that are listed in red and identified with issues (e.g., "cannot install"). Installation instructions to use this 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. It allows loading package from given directory: Thanks for contributing an answer to Stack Overflow! You can select a different mirror with chooseCRANmirror () and try the installation again. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. The package is in a non-standard repository. -- NN Ask Ubuntu is a question and answer site for Ubuntu users and developers. Why do small African island nations perform better than African continental nations, considering democracy and human development? Package fribidi was not found in the pkg-config search path. Can carbocations exist in a nonpolar solvent? Since this is a large matrix, you may wish to use the data viewer to examine it. Follow Up: struct sockaddr storage initialization by network format-string. The workaround is to set repository manually: This solution might break R but here is an easiest solution that works 99% of time. ==================================================, to the PKG_CONFIG_PATH environment variable, --------------------------- [ANTICONF] --------------------------------. Policy. package dataset is not available (for R version 3.1.1) Bioconductor release. Please clarify. I am trying to install DESeq2 and I keep getting errors. 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. (Yes/no/cancel) to which you have answered yes. package 'destiny' is not available for Bioconductor version '3.13
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