To learn more, see our tips on writing great answers. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. While a notebook is attached to a cluster, the R namespace cannot be refreshed. A place where magic is studied and practiced? May be the version has problem How can I do ? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 I've copied the output below in case it helps with troubleshooting. 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. One solution is to find all available packages. I just figured Id ask. Choose Yes. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. To learn more, see our tips on writing great answers. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? install.packages ("zip") When you load the package, you can observe this error. 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. 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: I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Looking for incompatible packages. 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 vegan) just to try it, does this inconvenience the caterers and staff? March 1, 2023, 4:56pm It only takes a minute to sign up. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. To resolve this error, install the required package as a cluster-installed library. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () New replies are no longer allowed. Not the answer you're looking for? Retrying with flexible solve.Solving environment: Found conflicts! problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied, BiocManager::install("XML") Making statements based on opinion; back them up with references or personal experience. to your account. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Learn more about Stack Overflow the company, and our products. @artembus Sounds like it was a ton of work! 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. March 1, 2023, 3:25pm This article explains how to resolve the package or namespace loading error. 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? Do I need a thermal expansion tank if I already have a pressure tank? Why are physically impossible and logically impossible concepts considered separate in terms of probability? package in your R session. 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. I tried following the instructions for 2019.7 as well and I am getting the same error. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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. Please try reinstalling rlang on a fresh session. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Thanks for contributing an answer to Stack Overflow! 0 packages out-of-date; 2 packages too new, BiocManager::install(c( The error states that the current version is 0.4.5 but 0.4.10 is required. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : 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. I guess that means we can finally close this issue. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Find centralized, trusted content and collaborate around the technologies you use most. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. 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. What is a word for the arcane equivalent of a monastery? Policy. (Factorization). Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. rev2023.3.3.43278. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Why is this sentence from The Great Gatsby grammatical? From the console install.packages ("rlang") should fix this. [7] datasets methods base, other attached packages: Is there anything I can do to speed it up? Installation instructions to use this I tried to download the "locfit" package but I can't find it anywhere. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Thanks! [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 The package has place the R version constraint. + ), update = TRUE, ask = FALSE) Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Installing package(s) 'htmlTable', 'xfun' Sounds like there might be an issue with conda setup? Policy. guide. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. 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. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? [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' 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 What is the output of. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) If not fixed, Try removing remove.packages (rlang) then. Is there a proper earth ground point in this switch box? MathJax reference. Surly Straggler vs. other types of steel frames. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. package rlang was built under R version 3.5.1. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( 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. 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. @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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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). 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'. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. If you preorder a special airline meal (e.g. Is there a single-word adjective for "having exceptionally strong moral principles"? 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. Use of this site constitutes acceptance of our User Agreement and Privacy Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Try again and choose No. When an R package depends on a newer package version, the required package is downloaded but not loaded. I was assuming that to be the case. Any other suggestion? Policy. 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. there is no package called data.table 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. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Also note, however, that the error you got has been associated in the past with mirror outages. Then I reinstalled R then Rstudio then RTools. Solving environment: Found conflicts! March 1, 2023, 8:52pm Convince your IT department to relax the permissions for R packages [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. 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. [7] edgeR_3.16.5 limma_3.30.12 Well occasionally send you account related emails. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Citation (from within R, enter citation ("DESeq2") ): Installation To install this package, start R (version "4.2") and enter: if (!require ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install ("DESeq2") For older versions of R, please refer to the appropriate Bioconductor release . installation of package GenomeInfoDbData had non-zero exit status. Sounds like you might have an issue with which R Rstudio is running. [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: R version 3.6.1 (2019-07-05) Is there a proper earth ground point in this switch box? 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. 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 . Platform: x86_64-apple-darwin17.0 (64-bit) [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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.