error: package or namespace load failed for 'deseq2

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Policy. Glad everything is finally working now. + "htmlTable", "xfun" Thanks for contributing an answer to Stack Overflow! 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. enter citation("DESeq2")): To install this package, start R (version I have tried your suggestion and also updating the packages that command indicates. Connect and share knowledge within a single location that is structured and easy to search. Should I update the Bioconductor to latest version instead? running multiple versions of the same package, keeping separate libraries for some projects). Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I thought that working in a new environment would help, but it didnt. [a/s/n]: 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. Fortunately I was able to solve it by doing things from several suggested solutions. A place where magic is studied and practiced? 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. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Can't Load R DESeq2 Library, Installed All Missing Packages and Still . [R] Error: package or namespace load failed for 'ggplot2' in trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' [40] assertthat_0.1 rpart_4.1-10 nnet_7.3-12, It should not be necessary (R should take care of loading dependencies) but try installating data.table also. When you load the package, you can observe this error. library(caret) namespace load failed Object sigma not How can I fix error with loading package in R ? | ResearchGate Content type 'application/zip' length 386703 bytes (377 KB) Installing package(s) 'XML' [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) When you load the package, you can observe this error. there is no package called locfit. I even tried BiocManager::install("XML") but all failed as shown below. Why is there a voltage on my HDMI and coaxial cables? While a notebook is attached to a cluster, the R namespace cannot be refreshed. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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 @artembus Sounds like it was a ton of work! 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. Thank you @hharder. 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]]): Is there anything I can do to speed it up? guide. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Use MathJax to format equations. - the incident has nothing to do with me; can I use this this way? It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Let me confer with the team. Whats the grammar of "For those whose stories they are"? Thnaks anyway, Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems, How Intuit democratizes AI development across teams through reusability. Warning message: sessionInfo() Running under: macOS Sierra 10.12.6. How do I align things in the following tabular environment? [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Warning: restored xfun, The downloaded binary packages are in Traffic: 307 users visited in the last hour, I am new to all this! To view documentation for the version of this package installed rev2023.3.3.43278. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 This topic was automatically closed 21 days after the last reply. rstudio - Error: package or namespace load failed for 'tidyverse Have a question about this project? there is no package called Hmisc. Use of this site constitutes acceptance of our User Agreement and Privacy If it fails, required operating system facilities are missing. So, supposedly the issue is with Hmisc. From the console install.packages ("rlang") should fix this. I installed the package successfully with conda, but Rstudio is apparently does not know about it. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. You are doing something very wrong when installing your packages. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat 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. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Retrying with flexible solve.Solving environment: Found conflicts! R version 3.6.3 (2020-02-29) By clicking Sign up for GitHub, you agree to our terms of service and Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) package xfun successfully unpacked and MD5 sums checked Statistics ; Algorithm(ML, DL,.) requires R 4 and running more than a couple of releases behind in R risks multiplying problems. So if you still get this error try changing your CRAN mirror. 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. Does anyone know why I'm getting the following message when I load tidyverse in a new session. I'm having a similar error, but different package: library("DESeq2") To learn more, see our tips on writing great answers. Is the God of a monotheism necessarily omnipotent? I just figured Id ask. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): 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]]) : [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Please remember to confirm an answer once you've received one. 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 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Open Source Biology & Genetics Interest Group. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Follow Up: struct sockaddr storage initialization by network format-string. and then updating the packages that command indicates. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Connect and share knowledge within a single location that is structured and easy to search. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' [7] edgeR_3.16.5 limma_3.30.12 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: May I know is there any other approach I can try? 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: 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. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? We've tried this - and can replicate this issue on a completely new install with no existing package installs. 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. This article explains how to resolve the package or namespace loading error. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Do I need a thermal expansion tank if I already have a pressure tank? One solution is to find all available packages. Use of this site constitutes acceptance of our User Agreement and Privacy Bioconductor - DESeq2 Policy. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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'. If not fixed, Try removing remove.packages (rlang) then. .onLoad failed in loadNamespace() for 'rlang', details: Feedback Sounds like you might have an issue with which R Rstudio is running. Give up and run everything from the "permitted" library location (e.g. Platform: x86_64-w64-mingw32/x64 (64-bit) library (olsrr) - Error - General - RStudio Community [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 It is working now. March 1, 2023, 3:25pm May be the version has problem How can I do ? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Surly Straggler vs. other types of steel frames. 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. In file.copy(savedcopy, lib, recursive = TRUE) : March 1, 2023, 8:52pm there is no package called GenomeInfoDbData 0 packages out-of-date; 2 packages too new, BiocManager::install(c( 1. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. And finally, install the problem packages, perhaps also DESeq2. The best answers are voted up and rise to the top, Not the answer you're looking for? Loading required package: GenomeInfoDb I highly recommend that any R/RStudio version not installed inside conda be removed. 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? downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. "4.2") and enter: For older versions of R, please refer to the appropriate More info about Internet Explorer and Microsoft Edge. C:\R\R-3.4.3\library). Any other suggestion? "After the incident", I started to be more careful not to trip over things. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. March 1, 2023, 4:56pm This includes any installed libraries. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so But I guess you have many problems with your installation, and I'd suggest. 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). Resolving package or namespace loading error Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Convince your IT department to relax the permissions for R packages Is a PhD visitor considered as a visiting scholar? Why do many companies reject expired SSL certificates as bugs in bug bounties? Then I reinstalled R then Rstudio then RTools. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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: [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Looking for incompatible packages.This can take several minutes. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. I hope you can see something I can't see and help me solving this issue. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. there is no package called data.table R version 4.0.1 (2020-06-06) error: object 'rlang_dots_list' not found Also note, however, that the error you got has been associated in the past with mirror outages. Surly Straggler vs. other types of steel frames. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Please read the posting I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. it would be good to hear any speculation you have of how this might have happened). Erasmus+ funds available! :), BiocManager::install("locift") To learn more, see our tips on writing great answers. 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. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 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 Is there anyone the same as mine error while loading library(DESeq2)? 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installing Hmisc as suggested above did not solve the issue. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. After 3-4 manual installs everything worked. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: How to use Slater Type Orbitals as a basis functions in matrix method correctly? [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Is there a proper earth ground point in this switch box? Sounds like there might be an issue with conda setup? I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. now when I tried installing the missing packages they did install. How can we prove that the supernatural or paranormal doesn't exist? Styling contours by colour and by line thickness in QGIS. Running under: Windows 10 x64 (build 18362), locale: Error when installing Aldex2 - Community Plugin Support - Open Source How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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. Acidity of alcohols and basicity of amines. 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. Is there a single-word adjective for "having exceptionally strong moral principles"? privacy statement. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Warning message: To resolve this error, install the required package as a cluster-installed library. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': I then launched the R application (from the finder, not RStudio) and installed BiocManager. 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. (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 . DESeq2 - I can't get the library to load - Bioconductor 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.