error: package or namespace load failed for 'deseq2 error: package or namespace load failed for 'deseq2

package in your R session. How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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]]) : Is a PhD visitor considered as a visiting scholar? [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 To resolve this error, install the required package as a cluster-installed library. March 1, 2023, 8:52pm Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. "After the incident", I started to be more careful not to trip over things. Connect and share knowledge within a single location that is structured and easy to search. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 there is no package called GenomeInfoDbData [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Styling contours by colour and by line thickness in QGIS. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Why is there a voltage on my HDMI and coaxial cables? This topic was automatically closed 21 days after the last reply. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 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]]): [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Update all/some/none? package rlang was built under R version 3.5.1. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Making statements based on opinion; back them up with references or personal experience. Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': + "htmlTable", "xfun" Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. If you preorder a special airline meal (e.g. Error: package GenomeInfoDb could not be loaded. Installing package(s) 'XML' 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 install.packages("BiocManager"), I get this error: R version 3.6.3 (2020-02-29) Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' From the console install.packages ("rlang") should fix this. 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Running under: macOS Sierra 10.12.6. I was assuming that to be the case. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 - the incident has nothing to do with me; can I use this this way? To add to this, I have also been using DESeq2 recently and ran into the same problem. 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 would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package. How do you ensure that a red herring doesn't violate Chekhov's gun? Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. + ), update = TRUE, ask = FALSE) Now loading the DESeq2 library (Errors): Because I already installed >10 packages by hand I assume the solution is not to keep installing the missing packages because those packages will have more missing packages and more and more and I won't get out of this loop. Find centralized, trusted content and collaborate around the technologies you use most. Are there tables of wastage rates for different fruit and veg? Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Running under: macOS Catalina 10.15.3, Matrix products: default Making statements based on opinion; back them up with references or personal experience. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) 4. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Please remember to confirm an answer once you've received one. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. ERROR: lazy loading failed for package Hmisc What is a word for the arcane equivalent of a monastery? [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Convince your IT department to relax the permissions for R packages Content type 'application/zip' length 233860 bytes (228 KB) 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. 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? I need help installing a package "DESeq2" having - RStudio Community 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. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( The package has place the R version constraint. Bioconductor release. 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. Just realize that I need to write the script "library("DESeq2")" before I proceed. The error states that the current version is 0.4.5 but 0.4.10 is required. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open Remember to always click on the red Show me the content on this page notice when navigating these older versions. What is the output of. When you load the package, you can observe this error. Warning: restored xfun, The downloaded binary packages are in [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 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. nnet, spatial, survival. in your system, start R and enter: Follow March 1, 2023, 3:25pm [16] phyloseq1.30.0, loaded via a namespace (and not attached): I do know that it works well in qiime2-2020.6. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Making statements based on opinion; back them up with references or personal experience. binary source needs_compilation 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. Platform: x86_64-apple-darwin17.0 (64-bit) Press CTRL-C to abort. nnet, spatial, survival [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. Post questions about Bioconductor Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Citation (from within R, Is there anything I can do to speed it up? 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. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Does anyone know why I'm getting the following message when I load tidyverse in a new session. DESeq2: Error: package or namespace load failed for 'DESeq2': objects library(caret) namespace load failed Object sigma not found caret , . Can't Load R DESeq2 Library, Installed All Missing Packages and Still Policy. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 How can I fix error with loading package in R ? | ResearchGate Are you sure the R you're running from the command line is installed through Anaconda as well? As such there are two solutions that may be more or less attainable given your own IT system. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Rload failed - You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' New replies are no longer allowed. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Content type 'application/zip' length 386703 bytes (377 KB) How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Finally After 3-4 manual installations of missing packages everything worked. sessionInfo() [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Open Source Biology & Genetics Interest Group. DESeq2 - I can't get the library to load - Bioconductor C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Is a PhD visitor considered as a visiting scholar? * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Try again and choose No. Any other suggestion? Does a summoned creature play immediately after being summoned by a ready action? I guess that means we can finally close this issue. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. To learn more, see our tips on writing great answers. biocLite(), install.packages() (and the devtools equivalent?) Choose Yes. No error messages are returned. I highly recommend that any R/RStudio version not installed inside conda be removed. Fortunately I was able to solve it by doing things from several suggested solutions. enter citation("DESeq2")): To install this package, start R (version Join us at CRISPR workshops in Koper, Slovenia in 2023. Also make sure that you have RTools.exe installed and working. But I guess you have many problems with your installation, and I'd suggest. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 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. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Follow Up: struct sockaddr storage initialization by network format-string. 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. 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. 2. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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: [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Whats the grammar of "For those whose stories they are"? Why do academics stay as adjuncts for years rather than move around? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 guide. [R] Error: package or namespace load failed for 'ggplot2' in survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Thanks! Find centralized, trusted content and collaborate around the technologies you use most. If not fixed, Try removing remove.packages (rlang) then. rev2023.3.3.43278. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Surly Straggler vs. other types of steel frames. Connect and share knowledge within a single location that is structured and easy to search. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 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") to allow custom library locations. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: ()library(DESeq2):Error in loadNamespace: no package called ""s Platform: x86_64-apple-darwin15.6.0 (64-bit) installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' DESeq2 installation in R - Bioconductor Is there a proper earth ground point in this switch box? a, There are binary versions available but the source versions are later: Is there anyone the same as mine error while loading library(DESeq2)? I tried to download the "locfit" package but I can't find it anywhere. install.packages ("zip") [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 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. package xfun successfully unpacked and MD5 sums checked However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Erasmus+ funds available! Loading required package: GenomicRanges (Factorization). I also tried something I found on google: but the installation had errors too, I can write them here if needed. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 I would like to install DESeq2 for DE analysis. Resolving package or namespace loading error Running under: Windows 10 x64 (build 18362), locale: The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Please try reinstalling rlang on a fresh session. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. 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: Should I update the Bioconductor to latest version instead? 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 . Warning message: in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy 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. [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: 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. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 rstudio - Error: package or namespace load failed for 'tidyverse [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Thanks for contributing an answer to Stack Overflow! Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Policy. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Policy. 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). Error when installing Aldex2 - Community Plugin Support - Open Source Content type 'application/zip' length 4255589 bytes (4.1 MB) A place where magic is studied and practiced? there is no package called GenomeInfoDbData The best answers are voted up and rise to the top, Not the answer you're looking for? @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. 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. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. March 1, 2023, 7:31pm 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 The other option is to download and older version of locfit from the package archive and install manually. You signed in with another tab or window. 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. 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. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 it would be good to hear any speculation you have of how this might have happened). BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub What do I need to do to reproduce your problem? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 1. .onLoad failed in loadNamespace() for 'rlang', details: Traffic: 307 users visited in the last hour, I am new to all this! /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Thanks for contributing an answer to Stack Overflow! By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Have you tried install.packages("locfit") ? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Not the answer you're looking for? I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Surly Straggler vs. other types of steel frames. 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.