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. Sounds like you might have an issue with which R Rstudio is running. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Content type 'application/zip' length 386703 bytes (377 KB) Also note, however, that the error you got has been associated in the past with mirror outages. 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. package rlang was built under R version 3.5.1. binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 In file.copy(savedcopy, lib, recursive = TRUE) : 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. package in your R session. Use MathJax to format equations. call: dots_list() I'm trying to reproduce your problem, so being as precise as possible is important. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Installing package(s) 'XML' [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [13] ggplot23.3.0 car3.0-7 carData3.0-3 to allow custom library locations. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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, object not found Whats the grammar of "For those whose stories they are"? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Surly Straggler vs. other types of steel frames. there is no package called GenomeInfoDbData Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") We've tried this - and can replicate this issue on a completely new install with no existing package installs. R version 3.6.1 (2019-07-05) 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 After 3-4 manual installs everything worked. 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 How to use Slater Type Orbitals as a basis functions in matrix method correctly? Join us at CRISPR workshops in Koper, Slovenia in 2023. Running under: macOS Catalina 10.15.3, Matrix products: default 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. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Running under: macOS Sierra 10.12.3, locale: now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Warning: restored xfun, The downloaded binary packages are in The package has place the R version constraint. there is no package called Hmisc. Glad everything is finally working now. Convince your IT department to relax the permissions for R packages I tried installing DESeq2 using: but it run into a lot of errors (some missing packages for some dependency packages etc) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files. Why is this sentence from The Great Gatsby grammatical? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. rev2023.3.3.43278. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). DESeq2: Error: package or namespace load failed for 'DESeq2': objects [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Solving environment: Found conflicts! library(caret) namespace load failed Object sigma not found caret , . My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Fortunately I was able to solve it by doing things from several suggested solutions. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. DESeq2 - I can't get the library to load - Bioconductor It only takes a minute to sign up. error: object 'rlang_dots_list' not found [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 and then updating the packages that command indicates. Running. Use of this site constitutes acceptance of our User Agreement and Privacy to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. rev2023.3.3.43278. 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). Warning message: I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. If you preorder a special airline meal (e.g. "4.2") and enter: For older versions of R, please refer to the appropriate To view documentation for the version of this package installed To resolve this error, install the required package as a cluster-installed library. This article explains how to resolve the package or namespace loading error. If you try loading the DEseq2 library now, that might work. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Is there anything I can do to speed it up? Try installing zip, and then loading olsrr. I've copied the output below in case it helps with troubleshooting. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Error when installing Aldex2 - Community Plugin Support - Open Source [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 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 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"). Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Installing Hmisc as suggested above did not solve the issue. Documentation Surly Straggler vs. other types of steel frames. "htmlTable", "xfun" /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages When you load the package, you can observe this error. ()library(DESeq2):Error in loadNamespace: no package called ""s (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 . install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Why do academics stay as adjuncts for years rather than move around? How can I fix error with loading package in R ? | ResearchGate 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"). Thanks for contributing an answer to Stack Overflow! LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open To learn more, see our tips on writing great answers. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 DESeq2 installation in R - Bioconductor Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Is there anyone the same as mine error while loading library(DESeq2)? [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in there is no package called GenomeInfoDbData Language(R, Python, SQL) Thanks! What do I need to do to reproduce your problem? Installation instructions to use this Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Why do academics stay as adjuncts for years rather than move around? [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 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. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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). [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 I just figured Id ask. 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. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [7] edgeR_3.16.5 limma_3.30.12 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. 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 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. I do know that it works well in qiime2-2020.6. :), BiocManager::install("locift") May be the version has problem How can I do ? Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' To learn more, see our tips on writing great answers. running multiple versions of the same package, keeping separate libraries for some projects). Install DESeq2 through anaconda - Bioinformatics Stack Exchange 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. [5] IRanges_2.8.1 S4Vectors_0.12.1 BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib . You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Platform: x86_64-apple-darwin15.6.0 (64-bit) March 1, 2023, 4:56pm - the incident has nothing to do with me; can I use this this way? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Post questions about Bioconductor More info about Internet Explorer and Microsoft Edge.

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