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. 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'. nnet, spatial, survival Sounds like there might be an issue with conda setup? [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 If you try loading the DEseq2 library now, that might work. Asking for help, clarification, or responding to other answers. Glad everything is finally working now. Surly Straggler vs. other types of steel frames. Sounds like you might have an issue with which R Rstudio is running. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Does anyone know why I'm getting the following message when I load tidyverse in a new session. Content type 'application/zip' length 4255589 bytes (4.1 MB) [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 nnet, spatial, survival. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. ERROR: dependency Hmisc is not available for package DESeq2 You signed in with another tab or window. "After the incident", I started to be more careful not to trip over things. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Warning message: Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Solution To resolve this error, install the required package as a cluster-installed library. [16] phyloseq1.30.0, loaded via a namespace (and not attached): downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Also note, however, that the error you got has been associated in the past with mirror outages. Fortunately I was able to solve it by doing things from several suggested solutions. Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. Use of this site constitutes acceptance of our User Agreement and Privacy To resolve this error, install the required package as a cluster-installed library. there is no package called GenomeInfoDbData Is a PhD visitor considered as a visiting scholar? 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. Why is there a voltage on my HDMI and coaxial cables? I highly recommend that any R/RStudio version not installed inside conda be removed. 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. I can download DESeq2 using, User Agreement and Privacy 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Policy. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Please read the posting 9. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: March 1, 2023, 7:31pm Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). package rlang was built under R version 3.5.1. 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") I tried again and again was met with missing packages BUT!!! How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Why are physically impossible and logically impossible concepts considered separate in terms of probability? /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages there is no package called GenomeInfoDbData + "htmlTable", "xfun" 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. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 How do you ensure that a red herring doesn't violate Chekhov's gun? Running. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Also make sure that you have RTools.exe installed and working. 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 Why do many companies reject expired SSL certificates as bugs in bug bounties? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 To learn more, see our tips on writing great answers. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . ERROR: lazy loading failed for package Hmisc How to notate a grace note at the start of a bar with lilypond? Not the answer you're looking for? 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. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Running under: macOS Sierra 10.12.6. Any suggestions would be greatly appreciated. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Please remember to confirm an answer once you've received one. it would be good to hear any speculation you have of how this might have happened). [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? I am running a new install of R (3.5.0) and RStudio (1.1.414). Bioconductor release. Follow Up: struct sockaddr storage initialization by network format-string. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 1. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Do I need a thermal expansion tank if I already have a pressure tank? 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? Have a question about this project? [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 2. Policy. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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 Running under: macOS Catalina 10.15.3, Matrix products: default Making statements based on opinion; back them up with references or personal experience. 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 The other option is to download and older version of locfit from the package archive and install manually. "After the incident", I started to be more careful not to trip over things. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib I then launched the R application (from the finder, not RStudio) and installed BiocManager. [69] tidyselect_1.0.0. there is no package called locfit. 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]]): Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Looking for incompatible packages.This can take several minutes. What is a word for the arcane equivalent of a monastery? That plugin is has not been updated to work with later releases of QIIME 2. 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 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. library(caret) namespace load failed Object sigma not found caret , . After 3-4 manual installs everything worked. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Installing package(s) 'GenomeInfoDbData' Open Source Biology & Genetics Interest Group. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. there is no package called Hmisc. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Erasmus+ funds available! Asking for help, clarification, or responding to other answers. Looking for incompatible packages. I would recommend installing an older version of QIIME 2 for this plugin to work. sessionInfo() Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide, You can try installing packages in R (which comes with R 3.5.1, not RStudio). Making statements based on opinion; back them up with references or personal experience. Documentation To learn more, see our tips on writing great answers. From the console install.packages ("rlang") should fix this. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Loading required package: GenomicRanges [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Why is this sentence from The Great Gatsby grammatical? sessionInfo() Loading required package: GenomeInfoDb Sign in Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Remember to always click on the red Show me the content on this page notice when navigating these older versions. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib library(DESeq2) [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Hello, Language(R, Python, SQL) Warning: cannot remove prior installation of package xfun [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Convince your IT department to relax the permissions for R packages 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. guide. rev2023.3.3.43278. 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. Making statements based on opinion; back them up with references or personal experience. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR MathJax reference. error: object 'rlang_dots_list' not found Why do academics stay as adjuncts for years rather than move around? [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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'. - the incident has nothing to do with me; can I use this this way? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. So if you still get this error try changing your CRAN mirror. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Installing package(s) 'htmlTable', 'xfun' [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Platform: x86_64-apple-darwin17.0 (64-bit) Connect and share knowledge within a single location that is structured and easy to search. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Already on GitHub? 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. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 You are doing something very wrong when installing your packages. 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)? So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. How to use Slater Type Orbitals as a basis functions in matrix method correctly? [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): [7] datasets methods base, other attached packages: Whats the grammar of "For those whose stories they are"? in your system, start R and enter: Follow Then I reinstalled R then Rstudio then RTools. Well occasionally send you account related emails. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Installing Hmisc as suggested above did not solve the issue. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Thank you @hharder. R version 4.0.1 (2020-06-06) 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. 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. It is working now. I installed the package successfully with conda, but Rstudio is apparently does not know about it. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 - the incident has nothing to do with me; can I use this this way? 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 . Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) A place where magic is studied and practiced? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. This article explains how to resolve the package or namespace loading error. Choose Yes. .onLoad failed in loadNamespace() for 'rlang', details: [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: Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): (Factorization). 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. Finally After 3-4 manual installations of missing packages everything worked. I tried following the instructions for 2019.7 as well and I am getting the same error. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. Start R to confirm they are gone. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () I hope you can see something I can't see and help me solving this issue. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. To add to this, I have also been using DESeq2 recently and ran into the same problem. I've copied the output below in case it helps with troubleshooting. I'm trying to reproduce your problem, so being as precise as possible is important. Use of this site constitutes acceptance of our User Agreement and Privacy It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Join us at CRISPR workshops in Koper, Slovenia in 2023. If you preorder a special airline meal (e.g. Running under: macOS Sierra 10.12.3, locale: 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. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 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 "4.2") and enter: For older versions of R, please refer to the appropriate Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? This topic was automatically closed 21 days after the last reply. package xfun successfully unpacked and MD5 sums checked running multiple versions of the same package, keeping separate libraries for some projects). [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 to allow custom library locations. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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. But I guess you have many problems with your installation, and I'd suggest. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. C:\R\R-3.4.3\library). 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installation instructions to use this New replies are no longer allowed. Citation (from within R, Does a summoned creature play immediately after being summoned by a ready action? so I would try to use BiocManager::install("XML"). in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I tried to download the "locfit" package but I can't find it anywhere. 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!!! Is the God of a monotheism necessarily omnipotent? 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?