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

The best answers are voted up and rise to the top, Not the answer you're looking for? @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. What is a word for the arcane equivalent of a monastery? The error states that the current version is 0.4.5 but 0.4.10 is required. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. I can download DESeq2 using, User Agreement and Privacy Installing DESeq2 Error: no package called GenomeInfoDbData, https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz, https://cran.rstudio.com/bin/macosx/contrib/4.0/RcppArmadillo_0.9.880.1.0.tgz, https://cran.rstudio.com/bin/macosx/contrib/4.0/survival_3.1-12.tgz. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Sounds like you might have an issue with which R Rstudio is running. If it fails, required operating system facilities are missing. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Finally After 3-4 manual installations of missing packages everything worked. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Error: package GenomeInfoDb could not be loaded. Then I reinstalled R then Rstudio then RTools. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. To add to this, I have also been using DESeq2 recently and ran into the same problem. Running under: Windows 10 x64 (build 18362), locale: Content type 'application/zip' length 4255589 bytes (4.1 MB) Is the God of a monotheism necessarily omnipotent? MathJax reference. 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 . It is working now. 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. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Use of this site constitutes acceptance of our User Agreement and Privacy [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Glad everything is finally working now. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 How do you ensure that a red herring doesn't violate Chekhov's gun? Looking for incompatible packages. [7] edgeR_3.16.5 limma_3.30.12 Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. enter citation("DESeq2")): To install this package, start R (version Installing package(s) 'htmlTable', 'xfun' Platform: x86_64-apple-darwin15.6.0 (64-bit) I then launched the R application (from the finder, not RStudio) and installed BiocManager. 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: Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6: https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip', User Agreement and Privacy Thanks for contributing an answer to Bioinformatics Stack Exchange! "After the incident", I started to be more careful not to trip over things. To view documentation for the version of this package installed You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Installing package(s) 'GenomeInfoDbData' Please read the posting Not the answer you're looking for? To learn more, see our tips on writing great answers. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. [13] ggplot23.3.0 car3.0-7 carData3.0-3 To learn more, see our tips on writing great answers. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. - the incident has nothing to do with me; can I use this this way? I highly recommend that any R/RStudio version not installed inside conda be removed. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? (Factorization). The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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. If you try loading the DEseq2 library now, that might work. Disconnect between goals and daily tasksIs it me, or the industry? :), BiocManager::install("locift") Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. + ), update = TRUE, ask = FALSE) As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. 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. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Start R to confirm they are gone. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 So, supposedly the issue is with Hmisc. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 R| - How to notate a grace note at the start of a bar with lilypond? library (olsrr) - Error - General - RStudio Community When an R package depends on a newer package version, the required package is downloaded but not loaded. there is no package called locfit. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Sounds like there might be an issue with conda setup? No error messages are returned. Can't Load R DESeq2 Library, Installed All Missing Packages and Still [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 @artembus Sounds like it was a ton of work! Content type 'application/zip' length 233860 bytes (228 KB) If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 9. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Is there anyone the same as mine error while loading library(DESeq2)? I tried to get a whole new environment and install an old version of Qiime but I still got a ton of conflicts and it didnt install. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Fortunately I was able to solve it by doing things from several suggested solutions. Warning: cannot remove prior installation of package xfun I also tried something I found on google: but the installation had errors too, I can write them here if needed. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. I was assuming that to be the case. Asking for help, clarification, or responding to other answers. Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. - the incident has nothing to do with me; can I use this this way? package xfun successfully unpacked and MD5 sums checked sessionInfo() [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Language(R, Python, SQL) [69] tidyselect_1.0.0. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Use of this site constitutes acceptance of our User Agreement and Privacy Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Sorry, I'm newbie. nnet, spatial, survival. New replies are no longer allowed. In file.copy(savedcopy, lib, recursive = TRUE) : Thank you @hharder. guide. March 1, 2023, 4:56pm [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Warning message: so I would try to use BiocManager::install("XML"). Open Source Biology & Genetics Interest Group. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Running under: macOS Sierra 10.12.3, locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8, attached base packages: installation of package GenomeInfoDbData had non-zero exit status. Hello, Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib I installed the package successfully with conda, but Rstudio is apparently does not know about it. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 I thought that working in a new environment would help, but it didnt. [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. 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. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. I tried following the instructions for 2019.7 as well and I am getting the same error. The package has place the R version constraint. biocLite(), install.packages() (and the devtools equivalent?) Solving environment: Found conflicts! Any other suggestion? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? How to use Slater Type Orbitals as a basis functions in matrix method correctly? Asking for help, clarification, or responding to other answers. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. In install.packages() : locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 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? running multiple versions of the same package, keeping separate libraries for some projects). [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 What is the output of. March 1, 2023, 7:31pm Just updated my previous R to 4.01 and now I cant load DESeq2. Is a PhD visitor considered as a visiting scholar? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? 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. Bioconductor - DESeq2 [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): I even tried BiocManager::install("XML") but all failed as shown below. Making statements based on opinion; back them up with references or personal experience. package in your R session. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. 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. 2. Statistics ; Algorithm(ML, DL,.) [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 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: in your system, start R and enter: Follow Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): We've tried this - and can replicate this issue on a completely new install with no existing package installs. [R] Error: package or namespace load failed for 'ggplot2' in By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. install.packages ("zip") 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Documentation Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. privacy statement. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? "After the incident", I started to be more careful not to trip over things. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Are there tables of wastage rates for different fruit and veg? Surly Straggler vs. other types of steel frames. 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]]) : Policy. I need help installing a package "DESeq2" having - RStudio Community 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 have tried your suggestion and also updating the packages that command indicates. I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! Follow Up: struct sockaddr storage initialization by network format-string. Acidity of alcohols and basicity of amines. A place where magic is studied and practiced? Platform: x86_64-apple-darwin13.4.0 (64-bit) Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Just realize that I need to write the script "library("DESeq2")" before I proceed. To subscribe to this RSS feed, copy and paste this URL into your RSS reader.