How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Language(R, Python, SQL) [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 ERROR: lazy loading failed for package Hmisc Bioconductor - DESeq2 I guess that means we can finally close this issue. 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 Are there tables of wastage rates for different fruit and veg? Running. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. DESeq2: Error: package or namespace load failed for 'DESeq2': objects From the console install.packages ("rlang") should fix this. Should I update the Bioconductor to latest version instead? I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Is there anyone the same as mine error while loading library(DESeq2)? I have tried your suggestion and also updating the packages that command indicates. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so . Thanks for contributing an answer to Bioinformatics Stack Exchange! [7] edgeR_3.16.5 limma_3.30.12 [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Disconnect between goals and daily tasksIs it me, or the industry? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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. Connect and share knowledge within a single location that is structured and easy to search. nnet, spatial, survival. if (!require("BiocManager", quietly = TRUE)) Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. So if you still get this error try changing your CRAN mirror. problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied, BiocManager::install("XML") /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Feedback Any suggestions would be greatly appreciated. I hope you can see something I can't see and help me solving this issue. (Factorization). [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 guide. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. How to use Slater Type Orbitals as a basis functions in matrix method correctly? Asking for help, clarification, or responding to other answers. When you load the package, you can observe this error. Then I reinstalled R then Rstudio then RTools. privacy statement. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. package xfun successfully unpacked and MD5 sums checked You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Try again and choose No. DESeq2 - I can't get the library to load - Bioconductor How can we prove that the supernatural or paranormal doesn't exist? Documentation ERROR: dependency Hmisc is not available for package DESeq2 What is the output of. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Warning message: to your account. Whats the grammar of "For those whose stories they are"? Have you tried install.packages("locfit") ? Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. rstudio - Error: package or namespace load failed for 'tidyverse Asking for help, clarification, or responding to other answers. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. 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'. Try installing zip, and then loading olsrr. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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 also tried something I found on google: but the installation had errors too, I can write them here if needed. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Follow Up: struct sockaddr storage initialization by network format-string. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 there is no package called GenomeInfoDbData survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): package rlang was built under R version 3.5.1. Content type 'application/zip' length 233860 bytes (228 KB) Error: package or namespace load failed for 'DESeq2 - Bioconductor 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. nnet, spatial, survival check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. data . In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. now when I tried installing the missing packages they did install. Connect and share knowledge within a single location that is structured and easy to search. Thnaks anyway, Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems, How Intuit democratizes AI development across teams through reusability. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Solution To resolve this error, install the required package as a cluster-installed library. Policy. CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. 4. Bad: conda install -c bioconda bioconductor-deseq2. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: This article explains how to resolve the package or namespace loading error. Platform: x86_64-w64-mingw32/x64 (64-bit) Retrying with flexible solve.Solving environment: Found conflicts! It only takes a minute to sign up. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? If not fixed, Try removing remove.packages (rlang) then. Give up and run everything from the "permitted" library location (e.g. 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. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. and then updating the packages that command indicates. More info about Internet Explorer and Microsoft Edge. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: 2. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Is there anything I can do to speed it up? 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. 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. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [13] ggplot23.3.0 car3.0-7 carData3.0-3 Thanks for contributing an answer to Stack Overflow! Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) rev2023.3.3.43278. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Use MathJax to format equations. Running under: macOS Sierra 10.12.6. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [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. Citation (from within R, Running under: macOS Catalina 10.15.3, Matrix products: default When an R package depends on a newer package version, the required package is downloaded but not loaded. Convince your IT department to relax the permissions for R packages [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 "After the incident", I started to be more careful not to trip over things. When an R package depends on a newer package version, the required package is downloaded but not loaded. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Let me confer with the team. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 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. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Use of this site constitutes acceptance of our User Agreement and Privacy Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Installing package(s) 'GenomeInfoDbData' Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, In file.copy(savedcopy, lib, recursive = TRUE) : New replies are no longer allowed. 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. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Please read the posting downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 R version 3.6.3 (2020-02-29) I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Warning message: Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? 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. I highly recommend that any R/RStudio version not installed inside conda be removed. Installing package(s) 'XML' Not the answer you're looking for? [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 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. 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. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? By clicking Sign up for GitHub, you agree to our terms of service and I installed the package successfully with conda, but Rstudio is apparently does not know about it. I thought that working in a new environment would help, but it didnt. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) :