error: package or namespace load failed for 'deseq2

Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Thanks for your suggestion. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): "After the incident", I started to be more careful not to trip over things. Have a question about this project? The best answers are voted up and rise to the top, Not the answer you're looking for? The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): How can I fix error with loading package in R ? | ResearchGate [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? May be the version has problem How can I do ? This topic was automatically closed 21 days after the last reply. Thanks for contributing an answer to Bioinformatics Stack Exchange! As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Do I need a thermal expansion tank if I already have a pressure tank? R| - [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. Why do academics stay as adjuncts for years rather than move around? 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? [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Why is this sentence from The Great Gatsby grammatical? 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. I need help installing a package "DESeq2" having - RStudio Community [69] tidyselect_1.0.0. Thanks for contributing an answer to Stack Overflow! so I would try to use BiocManager::install("XML"). [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 What am I doing wrong here in the PlotLegends specification? [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 @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. @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. Use this. Rload failed - You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Finally After 3-4 manual installations of missing packages everything worked. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Solution To resolve this error, install the required package as a cluster-installed library. and then updating the packages that command indicates. [7] edgeR_3.16.5 limma_3.30.12 rev2023.3.3.43278. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Choose Yes. 4. In install.packages() : R version 3.6.3 (2020-02-29) Use of this site constitutes acceptance of our User Agreement and Privacy Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? How do I align things in the following tabular environment? [R] Error: package or namespace load failed for 'ggplot2' in I tried to download the "locfit" package but I can't find it anywhere. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Use MathJax to format equations. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 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. Content type 'application/zip' length 386703 bytes (377 KB) package in your R session. error: object 'rlang_dots_list' not found R version 3.6.1 (2019-07-05) [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. 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 I'd take a look at need, to see if there are any insights to be had, so that you can correct the root problem rather than having to do this procedure with other packages. Solving environment: Found conflicts! [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 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 ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . I just figured Id ask. May I know is there any other approach I can try? March 1, 2023, 3:25pm Bioconductor release. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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]]) : Does a summoned creature play immediately after being summoned by a ready action? Is the God of a monotheism necessarily omnipotent? [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: By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. . To add to this, I have also been using DESeq2 recently and ran into the same problem. Sounds like there might be an issue with conda setup? You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Find centralized, trusted content and collaborate around the technologies you use most. nnet, spatial, survival. if (!require("BiocManager", quietly = TRUE)) Bioconductor - DESeq2 Is a PhD visitor considered as a visiting scholar? in your system, start R and enter: Follow To view documentation for the version of this package installed Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 1 RR. R https://www.jianshu.com/p/d9ca5a66cb72?v=1676346790161 2 ``` library (tidyverse) Error: package or namespace load failed for 'tidyverse' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'cli' 3.3.0>= 3.4.1 In addition: Warning message: You signed in with another tab or window. Any other suggestion? 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"). [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Find centralized, trusted content and collaborate around the technologies you use most. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 sessionInfo() ERROR: lazy loading failed for package Hmisc DESeq2 installation in R - Bioconductor [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 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. Content type 'application/zip' length 233860 bytes (228 KB) there is no package called locfit. I tried again and again was met with missing packages BUT!!! When you load the package, you can observe this error. 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. Try installing zip, and then loading olsrr. Why do academics stay as adjuncts for years rather than move around? Use of this site constitutes acceptance of our User Agreement and Privacy 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). 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages To learn more, see our tips on writing great answers. 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. New replies are no longer allowed. How do you ensure that a red herring doesn't violate Chekhov's gun? And finally, install the problem packages, perhaps also DESeq2. 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. Policy. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. DESeq2: Error: package or namespace load failed for 'DESeq2': objects By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. "After the incident", I started to be more careful not to trip over things. Is there a proper earth ground point in this switch box? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 rev2023.3.3.43278. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [13] ggplot23.3.0 car3.0-7 carData3.0-3 Did you do that? ()library(DESeq2):Error in loadNamespace: no package called ""s Not the answer you're looking for? Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Press CTRL-C to abort. Making statements based on opinion; back them up with references or personal experience. Thank you @hharder. Have you tried install.packages("locfit") ? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Is there anything I can do to speed it up? install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Use of this site constitutes acceptance of our User Agreement and Privacy Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") MathJax reference. Can't Load R DESeq2 Library, Installed All Missing Packages and Still + ), update = TRUE, ask = FALSE) [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Replacing broken pins/legs on a DIP IC package. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 I do know that it works well in qiime2-2020.6. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 to allow custom library locations. 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 I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Error when installing Aldex2 - Community Plugin Support - Open Source Well occasionally send you account related emails. This article explains how to resolve the package or namespace loading error. Styling contours by colour and by line thickness in QGIS. "htmlTable", "xfun" 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 hope you can see something I can't see and help me solving this issue. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. The other option is to download and older version of locfit from the package archive and install manually. to your account. Thanks for contributing an answer to Stack Overflow! Running under: Windows 10 x64 (build 18362), locale: Sounds like you might have an issue with which R Rstudio is running. 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. 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 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. 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 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. To learn more, see our tips on writing great answers. You are doing something very wrong when installing your packages. Learn more about Stack Overflow the company, and our products. Resolving package or namespace loading error a, There are binary versions available but the source versions are later: So if you still get this error try changing your CRAN mirror. Policy. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Please try the following steps: Quit all R/Rstudio sessions. "4.2") and enter: For older versions of R, please refer to the appropriate So, supposedly the issue is with Hmisc. What do I need to do to reproduce your problem? 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 . 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 there is no package called Hmisc. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. One solution is to find all available packages. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): If you preorder a special airline meal (e.g. 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. Loading required package: GenomeInfoDb It is working now. Error: package GenomeInfoDb could not be loaded. Installing Hmisc as suggested above did not solve the issue. 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 Sierra 10.12.6. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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.

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error: package or namespace load failed for 'deseq2