error: package or namespace load failed for 'deseq2 error: package or namespace load failed for 'deseq2

[13] ggplot23.3.0 car3.0-7 carData3.0-3 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 package rlang was built under R version 3.5.1. Making statements based on opinion; back them up with references or personal experience. Then I reinstalled R then Rstudio then RTools. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? March 1, 2023, 4:56pm 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User Agreement and Privacy :), BiocManager::install("locift") The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Making statements based on opinion; back them up with references or personal experience. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Solution To resolve this error, install the required package as a cluster-installed library. Then I reinstalled R then Rstudio then RTools. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 now when I tried installing the missing packages they did install. Please remember to confirm an answer once you've received one. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) We've tried this - and can replicate this issue on a completely new install with no existing package installs. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 I just figured Id ask. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. R version 3.6.3 (2020-02-29) Not the answer you're looking for? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Fortunately I was able to solve it by doing things from several suggested solutions. Asking for help, clarification, or responding to other answers. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 I then launched the R application (from the finder, not RStudio) and installed BiocManager. Loading required package: GenomeInfoDb 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. Please try the following steps: Quit all R/Rstudio sessions. there is no package called data.table Sign in Statistics ; Algorithm(ML, DL,.) Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. library ("DESeq2") 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 'Hmisc' Installing Hmisc as suggested above did not solve the issue. + "htmlTable", "xfun" Not the answer you're looking for? No error messages are returned. rev2023.3.3.43278. Does anyone know why I'm getting the following message when I load tidyverse in a new session. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): I would recommend installing an older version of QIIME 2 for this plugin to work. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages I want to import DESeq2 in Rstudio though and it is giving me a different error when I try importing DESeq2: Error in library("DESeq2") : there is no package called DESeq2. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Thanks for contributing an answer to Bioinformatics Stack Exchange! I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. 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 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]]): [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 library (olsrr) - Error - General - RStudio Community In install.packages() : What am I doing wrong here in the PlotLegends specification? Install DESeq2 through anaconda - Bioinformatics Stack Exchange Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Documentation [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Whats the grammar of "For those whose stories they are"? The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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. Surly Straggler vs. other types of steel frames. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. Rload failed - I would like to install DESeq2 for DE analysis. 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. 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. Powered by Discourse, best viewed with JavaScript enabled, DESeq2: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. [1] stats4 parallel stats graphics grDevices utils [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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). Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Are there tables of wastage rates for different fruit and veg? Are you sure the R you're running from the command line is installed through Anaconda as well? In addition: Warning message: It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Now loading the DESeq2 library (Errors): Because I already installed >10 packages by hand I assume the solution is not to keep installing the missing packages because those packages will have more missing packages and more and more and I won't get out of this loop. How to use Slater Type Orbitals as a basis functions in matrix method correctly? DESeq2 - I can't get the library to load - Bioconductor So, supposedly the issue is with Hmisc. Is there anyone the same as mine error while loading library(DESeq2)? @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. to your account. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Use of this site constitutes acceptance of our User Agreement and Privacy Find centralized, trusted content and collaborate around the technologies you use most. Why is this sentence from The Great Gatsby grammatical? Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Learn more about Stack Overflow the company, and our products. Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. . 9. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. When you load the package, you can observe this error. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat 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. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. ()library(DESeq2):Error in loadNamespace: no package called ""s Post questions about Bioconductor Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). [16] phyloseq1.30.0, loaded via a namespace (and not attached): How to notate a grace note at the start of a bar with lilypond? More info about Internet Explorer and Microsoft Edge. there is no package called GenomeInfoDbData Content type 'application/zip' length 4255589 bytes (4.1 MB) library(caret) namespace load failed Object sigma not found caret , . R version 3.6.1 (2019-07-05) How do I align things in the following tabular environment? [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. How can I fix error with loading package in R ? | ResearchGate there is no package called locfit. there is no package called Hmisc. I've copied the output below in case it helps with troubleshooting.