Join us at CRISPR workshops in Koper, Slovenia in 2023. package rlang was built under R version 3.5.1. sessionInfo() Also make sure that you have RTools.exe installed and working. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? rev2023.3.3.43278. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Are there tables of wastage rates for different fruit and veg? I would recommend installing an older version of QIIME 2 for this plugin to work. Connect and share knowledge within a single location that is structured and easy to search. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Making statements based on opinion; back them up with references or personal experience. Press CTRL-C to abort. Are you sure the R you're running from the command line is installed through Anaconda as well? Follow Up: struct sockaddr storage initialization by network format-string. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Just updated my previous R to 4.01 and now I cant load DESeq2. 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've previously written a blog post about this topic, and I can say from experience that installing R packages through conda can cause lots of headaches. 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 Use of this site constitutes acceptance of our User Agreement and Privacy [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 R version 3.6.3 (2020-02-29) Language(R, Python, SQL) "htmlTable", "xfun" What am I doing wrong here in the PlotLegends specification? The best answers are voted up and rise to the top, Not the answer you're looking for? 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. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked It only takes a minute to sign up. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under 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"). Use MathJax to format equations. 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: there is no package called GenomeInfoDbData Convince your IT department to relax the permissions for R packages Running under: macOS Catalina 10.15.3, Matrix products: default there is no package called GenomeInfoDbData I tried to download the "locfit" package but I can't find it anywhere. To view documentation for the version of this package installed I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. 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. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [a/s/n]: error: object 'rlang_dots_list' not found - the incident has nothing to do with me; can I use this this way? sessionInfo() Is a PhD visitor considered as a visiting scholar? vegan) just to try it, does this inconvenience the caterers and staff? [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Content type 'application/zip' length 233860 bytes (228 KB) Is there a single-word adjective for "having exceptionally strong moral principles"? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? [16] phyloseq1.30.0, loaded via a namespace (and not attached): Acidity of alcohols and basicity of amines. 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. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 (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 . Post questions about Bioconductor I do know that it works well in qiime2-2020.6. 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. and then updating the packages that command indicates. A place where magic is studied and practiced? You are doing something very wrong when installing your packages. May I know is there any other approach I can try? RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Start R to confirm they are gone. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Fortunately I was able to solve it by doing things from several suggested solutions. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 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 . 2. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. 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. Have you tried install.packages("locfit") ? 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). nnet, spatial, survival. 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'. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Policy. Learn more about Stack Overflow the company, and our products. Then I reinstalled R then Rstudio then RTools. Not the answer you're looking for? ERROR: lazy loading failed for package Hmisc Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Open Source Biology & Genetics Interest Group. 9. In file.copy(savedcopy, lib, recursive = TRUE) : call: dots_list() [1] stats4 parallel stats graphics grDevices utils [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Asking for help, clarification, or responding to other answers. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Installing package(s) 'GenomeInfoDbData' If you have a query related to it or one of the replies, start a new topic and refer back with a link. If you try loading the DEseq2 library now, that might work. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. Running under: Windows 10 x64 (build 18362), locale: Is there anyone the same as mine error while loading library(DESeq2)? Policy. 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. Hello, 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'. I even tried BiocManager::install("XML") but all failed as shown below. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Installation instructions to use this 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. Bad: conda install -c bioconda bioconductor-deseq2. Should I update the Bioconductor to latest version instead? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Try again and choose No. 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. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 there is no package called data.table [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. Looking for incompatible packages. Thank you @hharder. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Thanks! Making statements based on opinion; back them up with references or personal experience. a, There are binary versions available but the source versions are later: When you load the package, you can observe this error. [69] tidyselect_1.0.0. Give up and run everything from the "permitted" library location (e.g. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. What is a word for the arcane equivalent of a monastery? This can take several minutes. While a notebook is attached to a cluster, the R namespace cannot be refreshed. In addition: Warning message: I just figured Id ask. MathJax reference. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Does anyone know why I'm getting the following message when I load tidyverse in a new session. C:\R\R-3.4.3\library). 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 is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. As such there are two solutions that may be more or less attainable given your own IT system. Loading required package: GenomicRanges I am running a new install of R (3.5.0) and RStudio (1.1.414). downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in May be the version has problem How can I do ? install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat 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. there is no package called locfit. No error messages are returned. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 I am also encountering a set of similar (although possible totally unrelated) issue with other packages, RStudio provides the following warning every startup, library(devtools) gives the following errors, Someone on twitter asked for the results of packageDescription("rlang"). [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Sounds like you might have an issue with which R Rstudio is running. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. enter citation("DESeq2")): To install this package, start R (version In install.packages() : [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Making statements based on opinion; back them up with references or personal experience. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. rev2023.3.3.43278. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 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. By clicking Sign up for GitHub, you agree to our terms of service and I highly recommend that any R/RStudio version not installed inside conda be removed. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Just to add on -- do you require an old version of Bioconductor for your current project? One solution is to find all available packages. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. . Bioconductor release. How do you ensure that a red herring doesn't violate Chekhov's gun? 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. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Documentation I'm having a similar error, but different package: library("DESeq2") March 1, 2023, 4:56pm Platform: x86_64-apple-darwin13.4.0 (64-bit) [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 library(DESeq2) 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. Choose Yes. + ), update = TRUE, ask = FALSE) Do I need a thermal expansion tank if I already have a pressure tank? I tried following the instructions for 2019.7 as well and I am getting the same error. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. It is working now. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. nnet, spatial, survival Also note, however, that the error you got has been associated in the past with mirror outages. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 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. 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: Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. package xfun successfully unpacked and MD5 sums checked I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. 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. 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 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Please try the following steps: Quit all R/Rstudio sessions. So, supposedly the issue is with Hmisc. March 1, 2023, 3:25pm From the console install.packages ("rlang") should fix this. Is the God of a monotheism necessarily omnipotent? 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. 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. 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. Connect and share knowledge within a single location that is structured and easy to search. 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. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Why do academics stay as adjuncts for years rather than move around? 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. ERROR: dependency Hmisc is not available for package DESeq2 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. Find centralized, trusted content and collaborate around the technologies you use most. Please remember to confirm an answer once you've received one. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. there is no package called Hmisc. Surly Straggler vs. other types of steel frames. Is there a proper earth ground point in this switch box? Thanks for contributing an answer to Bioinformatics Stack Exchange! [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 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. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 New replies are no longer allowed. 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. R version 4.0.1 (2020-06-06) Solution To resolve this error, install the required package as a cluster-installed library. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Well occasionally send you account related emails. What do I need to do to reproduce your problem? This article explains how to resolve the package or namespace loading error. Erasmus+ funds available! If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : :), BiocManager::install("locift") Error: package GenomeInfoDb could not be loaded. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Policy. @KonradRudolph It's pacman (not packman) and you are correct in that it's basically just a wrapper for, Thanks for your suggestion, I tried doing this step by step as you said but the biocLite command still did throw errors for missing packages. Any suggestions would be greatly appreciated. Why are physically impossible and logically impossible concepts considered separate in terms of probability? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Connect and share knowledge within a single location that is structured and easy to search. Citation (from within R, if (!require("BiocManager", quietly = TRUE)) 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. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Why do academics stay as adjuncts for years rather than move around? 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. 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 Have a question about this project? 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 The package has place the R version constraint. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5