Installing package(s) 'XML' - the incident has nothing to do with me; can I use this this way? R version 3.6.1 (2019-07-05) Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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. In file.copy(savedcopy, lib, recursive = TRUE) : The error states that the current version is 0.4.5 but 0.4.10 is required. [13] ggplot23.3.0 car3.0-7 carData3.0-3 I highly recommend that any R/RStudio version not installed inside conda be removed. 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 And finally, install the problem packages, perhaps also DESeq2. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. No error messages are returned. This topic was automatically closed 21 days after the last reply. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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"). [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Why do academics stay as adjuncts for years rather than move around? 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. 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. Installing Hmisc as suggested above did not solve the issue. I have tried your suggestion and also updating the packages that command indicates. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [a/s/n]: To add to this, I have also been using DESeq2 recently and ran into the same problem. Find centralized, trusted content and collaborate around the technologies you use most. Thanks for your suggestion. Sorry, I'm newbie. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Just updated my previous R to 4.01 and now I cant load DESeq2. 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Warning: cannot remove prior installation of package xfun [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Running. I'm trying to reproduce your problem, so being as precise as possible is important. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : install.packages("BiocManager"), I get this error: [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 In addition: Warning message: sessionInfo() What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. install.packages ("zip") 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. 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in [5] IRanges_2.8.1 S4Vectors_0.12.1 ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR 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. 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 . [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Statistics ; Algorithm(ML, DL,.) How to use Slater Type Orbitals as a basis functions in matrix method correctly? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Also note, however, that the error you got has been associated in the past with mirror outages. I guess that means we can finally close this issue. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Styling contours by colour and by line thickness in QGIS. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Join us at CRISPR workshops in Koper, Slovenia in 2023. 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. Are there tables of wastage rates for different fruit and veg? [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 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. Looking for incompatible packages.This can take several minutes. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 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: Sounds like there might be an issue with conda setup? @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. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. nnet, spatial, survival. Content type 'application/zip' length 4255589 bytes (4.1 MB) a, There are binary versions available but the source versions are later: [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, 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]]): Do I need a thermal expansion tank if I already have a pressure tank? [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under To learn more, see our tips on writing great answers. 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]]) : 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. Thanks for contributing an answer to Stack Overflow! To view documentation for the version of this package installed Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Are you sure the R you're running from the command line is installed through Anaconda as well? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): .onLoad failed in loadNamespace() for 'rlang', details: 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. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Start R to confirm they are gone. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Is there a single-word adjective for "having exceptionally strong moral principles"? Choose Yes. I even tried BiocManager::install("XML") but all failed as shown below. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 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 Why do academics stay as adjuncts for years rather than move around? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. [7] datasets methods base, other attached packages: Policy. Surly Straggler vs. other types of steel frames. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. I tried to download the "locfit" package but I can't find it anywhere. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Warning: restored xfun, The downloaded binary packages are in [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Retrying with flexible solve.Solving environment: Found conflicts! It is working now. "After the incident", I started to be more careful not to trip over things. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. 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. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 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. Platform: x86_64-apple-darwin13.4.0 (64-bit) "After the incident", I started to be more careful not to trip over things. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Use this. I was assuming that to be the case. I tried following the instructions for 2019.7 as well and I am getting the same error. This can take several minutes. 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. + "htmlTable", "xfun" If it fails, required operating system facilities are missing. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Why do many companies reject expired SSL certificates as bugs in bug bounties? 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. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 [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. Is there anyone the same as mine error while loading library(DESeq2)? Policy. Error: package GenomeInfoDb could not be loaded. Please remember to confirm an answer once you've received one. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Content type 'application/zip' length 233860 bytes (228 KB) Documentation 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. Feedback [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Whats the grammar of "For those whose stories they are"? 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. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. While a notebook is attached to a cluster, the R namespace cannot be refreshed. 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. [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: Is it suspicious or odd to stand by the gate of a GA airport watching the planes? [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 library(DESeq2) How to use Slater Type Orbitals as a basis functions in matrix method correctly? I also tried something I found on google: but the installation had errors too, I can write them here if needed. 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. [1] stats4 parallel stats graphics grDevices utils Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so From the console install.packages ("rlang") should fix this. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I just figured Id ask. 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 you try loading the DEseq2 library now, that might work. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: When an R package depends on a newer package version, the required package is downloaded but not loaded. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Remember to always click on the red Show me the content on this page notice when navigating these older versions. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths.
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