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error: package or namespace load failed for 'deseq2

The error states that the current version is 0.4.5 but 0.4.10 is required. No error messages are returned. New replies are no longer allowed. Installing package(s) 'GenomeInfoDbData' [1] stats4 parallel stats graphics grDevices utils Use of this site constitutes acceptance of our User Agreement and Privacy + ), update = TRUE, ask = FALSE) @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. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. 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: In file.copy(savedcopy, lib, recursive = TRUE) : Disconnect between goals and daily tasksIs it me, or the industry? Installing package(s) 'XML' The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Then I reinstalled R then Rstudio then RTools. Making statements based on opinion; back them up with references or personal experience. Installing Hmisc as suggested above did not solve the issue. there is no package called GenomeInfoDbData Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) To view documentation for the version of this package installed More info about Internet Explorer and Microsoft Edge. Policy. Also make sure that you have RTools.exe installed and working. Please try reinstalling rlang on a fresh session. data . Just to add on -- do you require an old version of Bioconductor for your current project? Installation instructions to use this library (olsrr) - Error - General - RStudio Community So if you still get this error try changing your CRAN mirror. 4. Choose Yes. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 I guess that means we can finally close this issue. How can we prove that the supernatural or paranormal doesn't exist? - the incident has nothing to do with me; can I use this this way? 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. If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. Whats the grammar of "For those whose stories they are"? Open Source Biology & Genetics Interest Group. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 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. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 To add to this, I have also been using DESeq2 recently and ran into the same problem. 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. [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: in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Thanks for contributing an answer to Stack Overflow! Join us at CRISPR workshops in Koper, Slovenia in 2023. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Error: package GenomeInfoDb could not be loaded. What is the output of. Making statements based on opinion; back them up with references or personal experience. 1. How can I fix error with loading package in R ? | ResearchGate Documentation Then I reinstalled R then Rstudio then RTools. What is a word for the arcane equivalent of a monastery? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. March 1, 2023, 7:31pm I would like to install DESeq2 for DE analysis. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Not the answer you're looking for? Looking for incompatible packages. + "htmlTable", "xfun" Content type 'application/zip' length 386703 bytes (377 KB) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Use this. Start R to confirm they are gone. rev2023.3.3.43278. install.packages ("zip") I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Thank you @hharder. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' library(caret) namespace load failed Object sigma not found caret , . To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Also note, however, that the error you got has been associated in the past with mirror outages. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. The other option is to download and older version of locfit from the package archive and install manually. So, supposedly the issue is with Hmisc. 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"). /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () . 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. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. vegan) just to try it, does this inconvenience the caterers and staff? enter citation("DESeq2")): To install this package, start R (version "After the incident", I started to be more careful not to trip over things. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I thought that working in a new environment would help, but it didnt. When you load the package, you can observe this error. [5] IRanges_2.8.1 S4Vectors_0.12.1 Connect and share knowledge within a single location that is structured and easy to search. 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. Is there anyone the same as mine error while loading library(DESeq2)? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. 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. 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. "4.2") and enter: For older versions of R, please refer to the appropriate If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. 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. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Is a PhD visitor considered as a visiting scholar? If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : 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. sessionInfo() Traffic: 307 users visited in the last hour, I am new to all this! Following successful installation of backports BiocManager::install ("DESeq2") will succeed under What am I doing wrong here in the PlotLegends specification? Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? I need help installing a package "DESeq2" having - RStudio Community 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. 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. Install DESeq2 through anaconda - Bioinformatics Stack Exchange As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. library(DESeq2) Try installing zip, and then loading olsrr. I just figured Id ask. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Use of this site constitutes acceptance of our User Agreement and Privacy requires R 4 and running more than a couple of releases behind in R risks multiplying problems. package xfun successfully unpacked and MD5 sums checked 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. to allow custom library locations. Is there a proper earth ground point in this switch box? Policy. R version 3.6.3 (2020-02-29) Running. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Sounds like there might be an issue with conda setup? This topic was automatically closed 21 days after the last reply. Hello, 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. R DESeq2 - I am running a new install of R (3.5.0) and RStudio (1.1.414). You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages .onLoad failed in loadNamespace() for 'rlang', details: Should I update the Bioconductor to latest version instead? @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. Installing package(s) 'htmlTable', 'xfun' 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. binary source needs_compilation Please try the following steps: Quit all R/Rstudio sessions. The package has place the R version constraint. Statistics ; Algorithm(ML, DL,.) If you try loading the DEseq2 library now, that might work. 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 if (!require("BiocManager", quietly = TRUE)) As mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running). Warning message: I installed the package successfully with conda, but Rstudio is apparently does not know about it. ()library(DESeq2):Error in loadNamespace: no package called ""s 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. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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. Follow Up: struct sockaddr storage initialization by network format-string. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. 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]]) : DESeq2_2301_76497647-CSDN there is no package called Hmisc. I tried following the instructions for 2019.7 as well and I am getting the same error. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I can download DESeq2 using, User Agreement and Privacy Do I need a thermal expansion tank if I already have a pressure tank? 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 . [16] phyloseq1.30.0, loaded via a namespace (and not attached): That plugin is has not been updated to work with later releases of QIIME 2. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 By clicking Sign up for GitHub, you agree to our terms of service and [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Language(R, Python, SQL) 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. there is no package called GenomeInfoDbData Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? I'm having a similar error, but different package: library("DESeq2") nnet, spatial, survival If you have a query related to it or one of the replies, start a new topic and refer back with a link. When an R package depends on a newer package version, the required package is downloaded but not loaded. 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 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Policy. 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. Have you tried install.packages("locfit") ? I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. In install.packages() : Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. 9. 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). Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib '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. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Platform: x86_64-apple-darwin17.0 (64-bit) [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Running under: Windows 10 x64 (build 18362), locale: The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. How to use Slater Type Orbitals as a basis functions in matrix method correctly? a, There are binary versions available but the source versions are later: Platform: x86_64-apple-darwin13.4.0 (64-bit) I hope you can see something I can't see and help me solving this issue. Did you do that? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R

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