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

[1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 How can we prove that the supernatural or paranormal doesn't exist? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Just to add on -- do you require an old version of Bioconductor for your current project? Running under: macOS Sierra 10.12.3, locale: Have a question about this project? Join us at CRISPR workshops in Koper, Slovenia in 2023. Please remember to confirm an answer once you've received one. Surly Straggler vs. other types of steel frames. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 I guess that means we can finally close this issue. When an R package depends on a newer package version, the required package is downloaded but not loaded. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) "After the incident", I started to be more careful not to trip over things. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. After 3-4 manual installs everything worked. DESeq2 installation in R - Bioconductor Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. March 1, 2023, 3:25pm Solving environment: Found conflicts! :), BiocManager::install("locift") 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. + "htmlTable", "xfun" [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Policy. @artembus Sounds like it was a ton of work! [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Policy. Let me confer with the team. 9. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Statistics ; Algorithm(ML, DL,.) One solution is to find all available packages. 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. A place where magic is studied and practiced? Are you sure the R you're running from the command line is installed through Anaconda as well? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I'm trying to reproduce your problem, so being as precise as possible is important. I also tried something I found on google: but the installation had errors too, I can write them here if needed. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. - the incident has nothing to do with me; can I use this this way? Sounds like there might be an issue with conda setup? Can't Load R DESeq2 Library, Installed All Missing Packages and Still installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat R DESeq2 - library(DESeq2) [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Traffic: 307 users visited in the last hour, I am new to all this! [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Error: package GenomeInfoDb could not be loaded. C:\R\R-3.4.3\library). Give up and run everything from the "permitted" library location (e.g. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. guide. rev2023.3.3.43278. [5] IRanges_2.8.1 S4Vectors_0.12.1 locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 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. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Is a PhD visitor considered as a visiting scholar? [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 In addition: Warning message: 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in Bad: conda install -c bioconda bioconductor-deseq2. "4.2") and enter: For older versions of R, please refer to the appropriate Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Platform: x86_64-apple-darwin17.0 (64-bit) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 vegan) just to try it, does this inconvenience the caterers and staff? * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. No error messages are returned. (Factorization). requires R 4 and running more than a couple of releases behind in R risks multiplying problems. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Looking for incompatible packages.This can take several minutes. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib When you load the package, you can observe this error. Warning message: Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. 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'. there is no package called locfit. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 How do I align things in the following tabular environment? 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. (I have the most recent version of tidyverse, RStudio, and R.) Error: package or namespace load failed for 'tidyverse': .onAttach failed in attachNamespace() for 'tidyverse', details: call: glue(str, .envir = .envir, .transformer = transformer . Learn more about Stack Overflow the company, and our products. Making statements based on opinion; back them up with references or personal experience. Citation (from within R, enter citation ("DESeq2") ): Installation To install this package, start R (version "4.2") and enter: if (!require ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install ("DESeq2") For older versions of R, please refer to the appropriate Bioconductor release . [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Platform: x86_64-apple-darwin15.6.0 (64-bit) now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Styling contours by colour and by line thickness in QGIS. Running under: macOS Catalina 10.15.3, Matrix products: default To view documentation for the version of this package installed Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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]]): Content type 'application/zip' length 4255589 bytes (4.1 MB) [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: call: dots_list() What is the output of. 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. Error when installing Aldex2 - Community Plugin Support - Open Source By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Please try the following steps: Quit all R/Rstudio sessions. failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: q2-aldex2 -> python=3.6 Your python: python=3.8.15 Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Update all/some/none? install.packages("BiocManager"), I get this error: Making statements based on opinion; back them up with references or personal experience. R version 3.6.3 (2020-02-29) Installing Hmisc as suggested above did not solve the issue. Error: package or namespace load failed, object not found 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: Thanks! RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE in your system, start R and enter: Follow To learn more, see our tips on writing great answers. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Find centralized, trusted content and collaborate around the technologies you use most. If not fixed, Try removing remove.packages (rlang) then. Policy. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. .onLoad failed in loadNamespace() for 'rlang', details: 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). Installation instructions to use this Warning message: March 1, 2023, 8:52pm 1. It only takes a minute to sign up. data . May I know is there any other approach I can try? privacy statement. ()library(DESeq2):Error in loadNamespace: no package called ""s I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Use MathJax to format equations. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Choose Yes. 2. I would like to install DESeq2 for DE analysis. Feedback However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. I've copied the output below in case it helps with troubleshooting. To add to this, I have also been using DESeq2 recently and ran into the same problem. As such there are two solutions that may be more or less attainable given your own IT system. "After the incident", I started to be more careful not to trip over things. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open if (!require("BiocManager", quietly = TRUE)) March 1, 2023, 7:31pm library(caret) namespace load failed Object sigma not It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Rload failed - Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Already on GitHub? 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: Not the answer you're looking for? I would recommend installing an older version of QIIME 2 for this plugin to work. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Looking for incompatible packages. to allow custom library locations. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? DESeq2_2301_76497647-CSDN there is no package called data.table Loading required package: GenomeInfoDb /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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. Any other suggestion? 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. More info about Internet Explorer and Microsoft Edge. [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: Open Source Biology & Genetics Interest Group. It is working now. I need help installing a package "DESeq2" having - RStudio Community [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 The best answers are voted up and rise to the top, Not the answer you're looking for? sessionInfo() Connect and share knowledge within a single location that is structured and easy to search. By clicking Sign up for GitHub, you agree to our terms of service and 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) R version 4.0.1 (2020-06-06) I was assuming that to be the case. 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 'XML' so I would try to use BiocManager::install ("XML"). Connect and share knowledge within a single location that is structured and easy to search. [a/s/n]: Language(R, Python, SQL) Then I reinstalled R then Rstudio then RTools. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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"). nnet, spatial, survival Please read the posting I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. Install DESeq2 through anaconda - Bioinformatics Stack Exchange [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 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 [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 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. To resolve this error, install the required package as a cluster-installed library. error: object 'rlang_dots_list' not found The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Thanks for contributing an answer to Bioinformatics Stack Exchange! Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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. So, supposedly the issue is with Hmisc. rev2023.3.3.43278. Not the answer you're looking for? Convince your IT department to relax the permissions for R packages We've tried this - and can replicate this issue on a completely new install with no existing package installs. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' running multiple versions of the same package, keeping separate libraries for some projects). Whats the grammar of "For those whose stories they are"? When an R package depends on a newer package version, the required package is downloaded but not loaded.