error: package or namespace load failed for 'deseq2

- the incident has nothing to do with me; can I use this this way? I thought that working in a new environment would help, but it didnt. Remember to always click on the red Show me the content on this page notice when navigating these older versions. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Asking for help, clarification, or responding to other answers. Any other suggestion? [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: rev2023.3.3.43278. Why is there a voltage on my HDMI and coaxial cables? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Any suggestions would be greatly appreciated. rev2023.3.3.43278. install.packages("BiocManager"), I get this error: - the incident has nothing to do with me; can I use this this way? so I would try to use BiocManager::install("XML"). To view documentation for the version of this package installed In addition: Warning message: library(DESeq2) in your system, start R and enter: Follow The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Finally After 3-4 manual installations of missing packages everything worked. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. data . 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). If you preorder a special airline meal (e.g. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Fortunately I was able to solve it by doing things from several suggested solutions. Are you sure the R you're running from the command line is installed through Anaconda as well? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Whats the grammar of "For those whose stories they are"? ERROR: dependency Hmisc is not available for package DESeq2 [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat + "htmlTable", "xfun" Why do academics stay as adjuncts for years rather than move around? Running under: Windows 10 x64 (build 18362), locale: [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 (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 . 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 Not the answer you're looking for? [69] tidyselect_1.0.0. 2. Why do academics stay as adjuncts for years rather than move around? @artembus Sounds like it was a ton of work! R version 3.6.1 (2019-07-05) Thanks! [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: there is no package called GenomeInfoDbData [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' How to use Slater Type Orbitals as a basis functions in matrix method correctly? More info about Internet Explorer and Microsoft Edge. Please read the posting Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? I also tried something I found on google: but the installation had errors too, I can write them here if needed. Installing package(s) 'XML' 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'. 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 However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. I tried following the instructions for 2019.7 as well and I am getting the same error. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Language(R, Python, SQL) It only takes a minute to sign up. Open Source Biology & Genetics Interest Group. 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). @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. 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. I have tried your suggestion and also updating the packages that command indicates. rev2023.3.3.43278. March 1, 2023, 7:31pm No error messages are returned. Surly Straggler vs. other types of steel frames. Making statements based on opinion; back them up with references or personal experience. It is working now. If I run install.packages(GenomeInfoDb) from R console, it is telling me that the package is not available for R version 3.5.1. Traffic: 307 users visited in the last hour, I am new to all this! Looking for incompatible packages.This can take several minutes. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Styling contours by colour and by line thickness in QGIS. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. (Factorization). Looking for incompatible packages. 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. Choose Yes. When you load the package, you can observe this error. To learn more, see our tips on writing great answers. Use of this site constitutes acceptance of our User Agreement and Privacy "After the incident", I started to be more careful not to trip over things. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [1] stats4 parallel stats graphics grDevices utils "4.2") and enter: For older versions of R, please refer to the appropriate 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. This topic was automatically closed 21 days after the last reply. Use of this site constitutes acceptance of our User Agreement and Privacy install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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 Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 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. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 sessionInfo() [a/s/n]: [16] phyloseq1.30.0, loaded via a namespace (and not attached): Why is this sentence from The Great Gatsby grammatical? there is no package called locfit. Installing Hmisc as suggested above did not solve the issue. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. So if you still get this error try changing your CRAN mirror. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Thanks for your suggestion. I guess that means we can finally close this issue. 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. nnet, spatial, survival. Use MathJax to format equations. 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"). If not fixed, Try removing remove.packages (rlang) then. Installing package(s) 'htmlTable', 'xfun' Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) I do know that it works well in qiime2-2020.6. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 To resolve this error, install the required package as a cluster-installed library. Did you do that? Policy. "After the incident", I started to be more careful not to trip over things. Running under: macOS Catalina 10.15.3, Matrix products: default 0 packages out-of-date; 2 packages too new, BiocManager::install(c( it would be good to hear any speculation you have of how this might have happened). Policy. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. I would like to install DESeq2 for DE analysis. biocLite(), install.packages() (and the devtools equivalent?) Policy. if (!require("BiocManager", quietly = TRUE)) Making statements based on opinion; back them up with references or personal experience. Learn more about Stack Overflow the company, and our products. Please remember to confirm an answer once you've received one. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Acidity of alcohols and basicity of amines. Installation instructions to use this After 3-4 manual installs everything worked. [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: Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. [7] edgeR_3.16.5 limma_3.30.12 Content type 'application/zip' length 4255589 bytes (4.1 MB) Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Press CTRL-C to abort. That plugin is has not been updated to work with later releases of QIIME 2. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. When an R package depends on a newer package version, the required package is downloaded but not loaded. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Bad: conda install -c bioconda bioconductor-deseq2. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) We've tried this - and can replicate this issue on a completely new install with no existing package installs. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): 9. What is the output of. @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. + ), update = TRUE, ask = FALSE) Running under: macOS Sierra 10.12.3, locale: downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Sounds like you might have an issue with which R Rstudio is running. C:\R\R-3.4.3\library). This can take several minutes. I highly recommend that any R/RStudio version not installed inside conda be removed. You signed in with another tab or window. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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'm trying to reproduce your problem, so being as precise as possible is important. "htmlTable", "xfun" Does a summoned creature play immediately after being summoned by a ready action? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. accident on highway 21 texas today, worst neighborhoods in clearwater, fl, msc seashore room service menu,