error: package or namespace load failed for 'deseq2

[26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Use MathJax to format equations. if (!require("BiocManager", quietly = TRUE)) [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Thanks! there is no package called GenomeInfoDbData ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: 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. Start R to confirm they are gone. When you load the package, you can observe this error. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Please read the posting What am I doing wrong here in the PlotLegends specification? 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. and then updating the packages that command indicates. Old packages: 'RcppArmadillo', 'survival' [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 That plugin is has not been updated to work with later releases of QIIME 2. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Not the answer you're looking for? Bad: conda install -c bioconda bioconductor-deseq2. Does anyone know why I'm getting the following message when I load tidyverse in a new session. so I would try to use BiocManager::install("XML"). package in your R session. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Content type 'application/zip' length 233860 bytes (228 KB) Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? it would be good to hear any speculation you have of how this might have happened). Are you sure the R you're running from the command line is installed through Anaconda as well? Give up and run everything from the "permitted" library location (e.g. 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. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. How do you ensure that a red herring doesn't violate Chekhov's gun? Please try reinstalling rlang on a fresh session. 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. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib I have tried your suggestion and also updating the packages that command indicates. Update all/some/none? 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. Policy. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). To learn more, see our tips on writing great answers. 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"). May be the version has problem How can I do ? Policy. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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, There are binary versions available but the source versions are later: It only takes a minute to sign up. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Should I update the Bioconductor to latest version instead? The other option is to download and older version of locfit from the package archive and install manually. I would recommend installing an older version of QIIME 2 for this plugin to work. Have you tried install.packages("locfit") ? Use of this site constitutes acceptance of our User Agreement and Privacy "htmlTable", "xfun" Making statements based on opinion; back them up with references or personal experience. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: library(caret) namespace load failed Object sigma not found caret , . downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in 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. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked - the incident has nothing to do with me; can I use this this way? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Is a PhD visitor considered as a visiting scholar? error: object 'rlang_dots_list' not found install.packages ("zip") Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 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]]): If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 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. 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]]) : [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Also note, however, that the error you got has been associated in the past with mirror outages. Is a PhD visitor considered as a visiting scholar? 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. 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 Running under: macOS Sierra 10.12.6. How do I align things in the following tabular environment? 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 . Running under: macOS Catalina 10.15.3, Matrix products: default [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 @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. Sign in sessionInfo() [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Have a question about this project? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( 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. [5] IRanges_2.8.1 S4Vectors_0.12.1 Sounds like you might have an issue with which R Rstudio is running. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Then I reinstalled R then Rstudio then RTools. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Language(R, Python, SQL) The error states that the current version is 0.4.5 but 0.4.10 is required. Did you do that? Find centralized, trusted content and collaborate around the technologies you use most. How can we prove that the supernatural or paranormal doesn't exist? [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 While a notebook is attached to a cluster, the R namespace cannot be refreshed. nnet, spatial, survival Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. 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 . Connect and share knowledge within a single location that is structured and easy to search. Press CTRL-C to abort. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Then I reinstalled R then Rstudio then RTools. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. I even tried BiocManager::install("XML") but all failed as shown below. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Remember to always click on the red Show me the content on this page notice when navigating these older versions. What is a word for the arcane equivalent of a monastery? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Policy. 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. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 If it fails, required operating system facilities are missing. I'd take a look at need, to see if there are any insights to be had, so that you can correct the root problem rather than having to do this procedure with other packages. Thank you @hharder. install.packages("BiocManager"), I get this error: I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. I just figured Id ask. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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: Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) As such there are two solutions that may be more or less attainable given your own IT system. 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. 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 In addition: Warning message: R version 4.0.1 (2020-06-06) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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: However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. 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). C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages R version 3.6.3 (2020-02-29) [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 now when I tried installing the missing packages they did install. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Installing package(s) 'htmlTable', 'xfun' So, supposedly the issue is with Hmisc. [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: RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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. there is no package called data.table Retrying with flexible solve.Solving environment: Found conflicts! How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Citation (from within R, 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: rev2023.3.3.43278. + "htmlTable", "xfun" Well occasionally send you account related emails. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Running under: Windows 10 x64 (build 18362), locale: BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Platform: x86_64-apple-darwin13.4.0 (64-bit) Making statements based on opinion; back them up with references or personal experience. "After the incident", I started to be more careful not to trip over things. Please remember to confirm an answer once you've received one. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Asking for help, clarification, or responding to other answers. Glad everything is finally working now. there is no package called locfit. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? The best answers are voted up and rise to the top, Not the answer you're looking for? I do know that it works well in qiime2-2020.6. Fortunately I was able to solve it by doing things from several suggested solutions. 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'. 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. Is there anything I can do to speed it up? Use of this site constitutes acceptance of our User Agreement and Privacy 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 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. You signed in with another tab or window. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Acidity of alcohols and basicity of amines. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () there is no package called GenomeInfoDbData 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. 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. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [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. (Factorization). If you have a query related to it or one of the replies, start a new topic and refer back with a link. privacy statement. Whats the grammar of "For those whose stories they are"? After 3-4 manual installs everything worked. Convince your IT department to relax the permissions for R packages 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. Is there a single-word adjective for "having exceptionally strong moral principles"? [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 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. Installing package(s) 'XML' C:\R\R-3.4.3\library). Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Policy. 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. I also tried something I found on google: but the installation had errors too, I can write them here if needed. What do I need to do to reproduce your problem? 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? The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? "After the incident", I started to be more careful not to trip over things. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Thanks for contributing an answer to Stack Overflow! [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 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. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? ERROR: lazy loading failed for package Hmisc Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Content type 'application/zip' length 4255589 bytes (4.1 MB) Solving environment: Found conflicts! 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. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 If you try loading the DEseq2 library now, that might work. Join us at CRISPR workshops in Koper, Slovenia in 2023. If not fixed, Try removing remove.packages (rlang) then. 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. I hope you can see something I can't see and help me solving this issue. Warning message: One solution is to find all available packages. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): I installed the package successfully with conda, but Rstudio is apparently does not know about it. Also make sure that you have RTools.exe installed and working. 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.