R version 4.0.1 (2020-06-06) I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. now when I tried installing the missing packages they did install. When you load the package, you can observe this error. Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. Policy. Language(R, Python, SQL) sessionInfo() Follow Up: struct sockaddr storage initialization by network format-string. Solution To resolve this error, install the required package as a cluster-installed library. Install DESeq2 through anaconda - Bioinformatics Stack Exchange Then I reinstalled R then Rstudio then RTools. If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. I even tried BiocManager::install("XML") but all failed as shown below. if (!require("BiocManager", quietly = TRUE)) Warning message: Can't Load R DESeq2 Library, Installed All Missing Packages and Still You are doing something very wrong when installing your packages. What am I doing wrong here in the PlotLegends specification? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Find centralized, trusted content and collaborate around the technologies you use most. Please try the following steps: Quit all R/Rstudio sessions. Just to add on -- do you require an old version of Bioconductor for your current project? Replacing broken pins/legs on a DIP IC package. I tried installing DESeq2 using: but it run into a lot of errors (some missing packages for some dependency packages etc) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files. I can download DESeq2 using, User Agreement and Privacy As mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running). locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. By clicking Sign up for GitHub, you agree to our terms of service and I hope you can see something I can't see and help me solving this issue. How can we prove that the supernatural or paranormal doesn't exist? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Installation instructions to use this I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 nnet, spatial, survival. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called locfit, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? [7] datasets methods base, other attached packages: rstudio - Error: package or namespace load failed for 'tidyverse [40] assertthat_0.1 rpart_4.1-10 nnet_7.3-12, It should not be necessary (R should take care of loading dependencies) but try installating data.table also. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' As such there are two solutions that may be more or less attainable given your own IT system. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Not the answer you're looking for? Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) R version 3.6.1 (2019-07-05) So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Installing package(s) 'htmlTable', 'xfun' I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. there is no package called Hmisc. Styling contours by colour and by line thickness in QGIS. Bioconductor release. running multiple versions of the same package, keeping separate libraries for some projects). @Tung I've updated my R and RStudio versions (unfortunately I had to first convince my workplace to approve them) and installed the packages through R 3.5.1 however, I'm still getting the same rlang error. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 Statistics ; Algorithm(ML, DL,.) Learn more about Stack Overflow the company, and our products. Connect and share knowledge within a single location that is structured and easy to search. package in your R session. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' but when I go to load the libraries I get this error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Not the answer you're looking for? Thanks for your suggestion. I am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 R DESeq2 - After 3-4 manual installs everything worked. We've tried this - and can replicate this issue on a completely new install with no existing package installs. 2. Warning message: Asking for help, clarification, or responding to other answers. Warning: cannot remove prior installation of package xfun Remember to always click on the red Show me the content on this page notice when navigating these older versions. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 It only takes a minute to sign up. 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. privacy statement. Looking for incompatible packages. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : ERROR: lazy loading failed for package Hmisc Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. ()library(DESeq2):Error in loadNamespace: no package called ""s Retrying with flexible solve.Solving environment: Found conflicts! When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. Bioconductor - DESeq2 Error when installing Aldex2 - Community Plugin Support - Open Source Have you tried install.packages("locfit") ? What is the output of. so I would try to use BiocManager::install("XML"). By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Running under: macOS Sierra 10.12.6. Open Source Biology & Genetics Interest Group. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. Why is there a voltage on my HDMI and coaxial cables? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Hello, sessionInfo() Old packages: 'RcppArmadillo', 'survival' I am also encountering a set of similar (although possible totally unrelated) issue with other packages, RStudio provides the following warning every startup, library(devtools) gives the following errors, Someone on twitter asked for the results of packageDescription("rlang"). Sorry if I missed this, the question was quite long so I kind of skimmed, but I noticed that early on some of the packages were reported as requiring manual compilation from source. I thought that working in a new environment would help, but it didnt. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit?
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