Update all/some/none? 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 I thought that working in a new environment would help, but it didnt. Please try the following steps: Quit all R/Rstudio sessions. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 I would like to install DESeq2 for DE analysis. - the incident has nothing to do with me; can I use this this way? [16] phyloseq1.30.0, loaded via a namespace (and not attached): [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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. I'm trying to reproduce your problem, so being as precise as possible is important. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [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. 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. nnet, spatial, survival 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. Resolving package or namespace loading error Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): nnet, spatial, survival. More info about Internet Explorer and Microsoft Edge. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Let me confer with the team. 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. library(DESeq2) 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'. Connect and share knowledge within a single location that is structured and easy to search. Making statements based on opinion; back them up with references or personal experience. When an R package depends on a newer package version, the required package is downloaded but not loaded. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 there is no package called Hmisc. While a notebook is attached to a cluster, the R namespace cannot be refreshed. You are doing something very wrong when installing your packages. 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. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. If you have a query related to it or one of the replies, start a new topic and refer back with a link. I have tried your suggestion and also updating the packages that command indicates. Start R to confirm they are gone. Bad: conda install -c bioconda bioconductor-deseq2. Why do academics stay as adjuncts for years rather than move around? [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Glad everything is finally working now. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Is there a proper earth ground point in this switch box? 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? R| - Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Thanks for contributing an answer to Bioinformatics Stack Exchange! install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Just realize that I need to write the script "library("DESeq2")" before I proceed. 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. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Use of this site constitutes acceptance of our User Agreement and Privacy dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext In file.copy(savedcopy, lib, recursive = TRUE) : 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 Is a PhD visitor considered as a visiting scholar? [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Try again and choose No. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. [R] Error: package or namespace load failed for 'ggplot2' in .onLoad failed in loadNamespace() for 'rlang', details: [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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. so I would try to use BiocManager::install("XML"). Acidity of alcohols and basicity of amines. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 ()library(DESeq2):Error in loadNamespace: no package called ""s Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Policy. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Press CTRL-C to abort. 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. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat it would be good to hear any speculation you have of how this might have happened). installation of package GenomeInfoDbData had non-zero exit status. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). "4.2") and enter: For older versions of R, please refer to the appropriate Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . R version 3.6.3 (2020-02-29) @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. The package has place the R version constraint. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Convince your IT department to relax the permissions for R packages Citation (from within R, DESeq2 - I can't get the library to load - Bioconductor I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. 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. error: object 'rlang_dots_list' not found [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Loading required package: GenomicRanges What am I doing wrong here in the PlotLegends specification? Solving environment: Found conflicts! We've tried this - and can replicate this issue on a completely new install with no existing package installs. Retrying with flexible solve.Solving environment: Found conflicts! 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. Should I update the Bioconductor to latest version instead? March 1, 2023, 3:25pm I even tried BiocManager::install("XML") but all failed as shown below. 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. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Error: package or namespace load failed, object not found Not the answer you're looking for? In addition: Warning message: 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. 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 rev2023.3.3.43278. Statistics ; Algorithm(ML, DL,.) Sign in install.packages ("zip") Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. and then updating the packages that command indicates. library(caret) namespace load failed Object sigma not Policy. biocLite(), install.packages() (and the devtools equivalent?) Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. I do know that it works well in qiime2-2020.6. Installing package(s) 'XML' Loading required package: GenomeInfoDb How can I fix error with loading package in R ? | ResearchGate Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR I installed the package successfully with conda, but Rstudio is apparently does not know about it. Use of this site constitutes acceptance of our User Agreement and Privacy rstudio - Error: package or namespace load failed for 'tidyverse Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Installing package(s) 'GenomeInfoDbData' Is there a proper earth ground point in this switch box? [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: In install.packages() : 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 . 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. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Can't Load R DESeq2 Library, Installed All Missing Packages and Still 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). Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Open Source Biology & Genetics Interest Group. Follow Up: struct sockaddr storage initialization by network format-string. Running. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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]]): + ), update = TRUE, ask = FALSE) Choose Yes. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Connect and share knowledge within a single location that is structured and easy to search. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 To learn more, see our tips on writing great answers. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages By clicking Sign up for GitHub, you agree to our terms of service and [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Installation instructions to use this Do I need a thermal expansion tank if I already have a pressure tank? Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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). Content type 'application/zip' length 233860 bytes (228 KB) 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). + "htmlTable", "xfun" Warning message: Is there anyone the same as mine error while loading library(DESeq2)? This includes any installed libraries. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. rev2023.3.3.43278. The error states that the current version is 0.4.5 but 0.4.10 is required. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. (Factorization). [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Platform: x86_64-apple-darwin17.0 (64-bit) 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]]) : Please remember to confirm an answer once you've received one. package in your R session. Running under: Windows 10 x64 (build 18362), locale: I highly recommend that any R/RStudio version not installed inside conda be removed. Sounds like there might be an issue with conda setup? 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 think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. To view documentation for the version of this package installed You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. 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 a PhD visitor considered as a visiting scholar? [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 R version 3.6.1 (2019-07-05) What is the output of. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. 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. Solution To resolve this error, install the required package as a cluster-installed library. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? How to use Slater Type Orbitals as a basis functions in matrix method correctly? [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Making statements based on opinion; back them up with references or personal experience. To learn more, see our tips on writing great answers. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. [13] ggplot23.3.0 car3.0-7 carData3.0-3 [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib When you load the package, you can observe this error. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 to allow custom library locations. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Is there anything I can do to speed it up? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. if (!require("BiocManager", quietly = TRUE))
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