error: package or namespace load failed for 'deseq2

This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Try again and choose No. Warning message: Surly Straggler vs. other types of steel frames. Installing package(s) 'GenomeInfoDbData' Start R to confirm they are gone. C:\R\R-3.4.3\library). [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 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 . 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]]): Why do academics stay as adjuncts for years rather than move around? No error messages are returned. @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. 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]]) : What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Connect and share knowledge within a single location that is structured and easy to search. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 9. MathJax reference. Choose Yes. 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. Is the God of a monotheism necessarily omnipotent? Thanks for contributing an answer to Bioinformatics Stack Exchange! Please try the following steps: Quit all R/Rstudio sessions. 2. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. If it fails, required operating system facilities are missing. ERROR: dependency Hmisc is not available for package DESeq2 But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. Running under: macOS Sierra 10.12.6. March 1, 2023, 4:56pm You signed in with another tab or window. R version 3.6.1 (2019-07-05) Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Replacing broken pins/legs on a DIP IC package. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Do I need a thermal expansion tank if I already have a pressure tank? Is a PhD visitor considered as a visiting scholar? Then I reinstalled R then Rstudio then RTools. rev2023.3.3.43278. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Use this. rev2023.3.3.43278. 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 'XML' so I would try to use BiocManager::install ("XML"). If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : 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. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [69] tidyselect_1.0.0. How to notate a grace note at the start of a bar with lilypond? privacy statement. Platform: x86_64-w64-mingw32/x64 (64-bit) Warning: cannot remove prior installation of package xfun 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. 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. 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 . What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? I was assuming that to be the case. From the console install.packages ("rlang") should fix this. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 How to use Slater Type Orbitals as a basis functions in matrix method correctly? [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: now when I tried installing the missing packages they did install. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 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. March 1, 2023, 3:25pm Policy. Any other suggestion? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Running under: macOS Catalina 10.15.3, Matrix products: default Is a PhD visitor considered as a visiting scholar? That plugin is has not been updated to work with later releases of QIIME 2. What do I need to do to reproduce your problem? 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. Use of this site constitutes acceptance of our User Agreement and Privacy I installed the package successfully with conda, but Rstudio is apparently does not know about it. What am I doing wrong here in the PlotLegends specification? Just realize that I need to write the script "library("DESeq2")" before I proceed. Connect and share knowledge within a single location that is structured and easy to search. Content type 'application/zip' length 233860 bytes (228 KB) March 1, 2023, 8:52pm To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Sounds like there might be an issue with conda setup? a, There are binary versions available but the source versions are later: 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. A place where magic is studied and practiced? [7] edgeR_3.16.5 limma_3.30.12 The other option is to download and older version of locfit from the package archive and install manually. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Policy. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 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. Learn more about Stack Overflow the company, and our products. I would recommend installing an older version of QIIME 2 for this plugin to work. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Looking for incompatible packages. Making statements based on opinion; back them up with references or personal experience. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Should I update the Bioconductor to latest version instead? 4. I'm trying to reproduce your problem, so being as precise as possible is important. Why is this sentence from The Great Gatsby grammatical? Bad: conda install -c bioconda bioconductor-deseq2. I tried following the instructions for 2019.7 as well and I am getting the same error. biocLite(), install.packages() (and the devtools equivalent?) [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Please try reinstalling rlang on a fresh session. + ), update = TRUE, ask = FALSE) Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' It only takes a minute to sign up. if (!require("BiocManager", quietly = TRUE)) Update all/some/none? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Installing Hmisc as suggested above did not solve the issue. Please remember to confirm an answer once you've received one. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Policy. 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. .onLoad failed in loadNamespace() for 'rlang', details: In addition: Warning message: (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 . Is there a proper earth ground point in this switch box? [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 In file.copy(savedcopy, lib, recursive = TRUE) : nnet, spatial, survival How to use Slater Type Orbitals as a basis functions in matrix method correctly? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Language(R, Python, SQL) Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. After 3-4 manual installs everything worked. 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). [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): 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. I highly recommend that any R/RStudio version not installed inside conda be removed. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. it would be good to hear any speculation you have of how this might have happened). I have tried your suggestion and also updating the packages that command indicates. 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: [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: 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. 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 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. Use MathJax to format equations. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 installation of package GenomeInfoDbData had non-zero exit status. Solving environment: Found conflicts! survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy.

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