Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib C:\R\R-3.4.3\library). "After the incident", I started to be more careful not to trip over things. 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'. 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"). What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Platform: x86_64-w64-mingw32/x64 (64-bit) [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Does a summoned creature play immediately after being summoned by a ready action? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Is a PhD visitor considered as a visiting scholar? Not the answer you're looking for? Loading required package: GenomicRanges Can't Load R DESeq2 Library, Installed All Missing Packages and Still [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Running under: macOS Sierra 10.12.6. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Browse other questions tagged, 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. biocLite(), install.packages() (and the devtools equivalent?) Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. To view documentation for the version of this package installed If not fixed, Try removing remove.packages (rlang) then. Is a PhD visitor considered as a visiting scholar? Whats the grammar of "For those whose stories they are"? Is there a proper earth ground point in this switch box? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? I would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package. 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]]) : Sorry, I'm newbie. May I know is there any other approach I can try? From the console install.packages ("rlang") should fix this. Content type 'application/zip' length 386703 bytes (377 KB) Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Let me confer with the team. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Just realize that I need to write the script "library("DESeq2")" before I proceed. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Installing package(s) 'GenomeInfoDbData' By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Well occasionally send you account related emails. Asking for help, clarification, or responding to other answers. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 nnet, spatial, survival. I tried following the instructions for 2019.7 as well and I am getting the same error. New replies are no longer allowed. In addition: Warning message: Update all/some/none? Find centralized, trusted content and collaborate around the technologies you use most. Please read the posting Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. What do I need to do to reproduce your 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Thanks for contributing an answer to Bioinformatics Stack Exchange! 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]]): Making statements based on opinion; back them up with references or personal experience. I hope you can see something I can't see and help me solving this issue. Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace (i, c (lib.loc, .libPaths ()), versionCheck = vI [ [i]]): there is no package called 'GenomeInfoDbData' Error: package 'GenomeInfoDb' could not be loaded When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. But I guess you have many problems with your installation, and I'd suggest. This article explains how to resolve the package or namespace loading error. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Running under: Windows 10 x64 (build 18362), locale: [13] ggplot23.3.0 car3.0-7 carData3.0-3 @KonradRudolph It's pacman (not packman) and you are correct in that it's basically just a wrapper for, Thanks for your suggestion, I tried doing this step by step as you said but the biocLite command still did throw errors for missing packages. The best answers are voted up and rise to the top, Not the answer you're looking for? :), BiocManager::install("locift") Fortunately I was able to solve it by doing things from several suggested solutions. [7] datasets methods base, other attached packages: Author: Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd], Maintainer: Michael Love . Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) package in your R session. March 1, 2023, 7:31pm To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [69] tidyselect_1.0.0. Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. there is no package called GenomeInfoDbData [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: downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Solution To resolve this error, install the required package as a cluster-installed library. 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. As such there are two solutions that may be more or less attainable given your own IT system. This topic was automatically closed 21 days after the last reply. Any other suggestion? 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' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. That plugin is has not been updated to work with later releases of QIIME 2. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Traffic: 307 users visited in the last hour, I am new to all this! [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. Language(R, Python, SQL) Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. 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: ERROR: lazy loading failed for package Hmisc Disconnect between goals and daily tasksIs it me, or the industry? Looking for incompatible packages.This can take several minutes. 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. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. This is the beauty of installing QIIME 2 via conda, you can have many different versions of QIIME 2 on your system at the same time and activate the version you want to use. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7