Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. 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") Find centralized, trusted content and collaborate around the technologies you use most. 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. Installing package(s) 'XML' Sorry, I'm newbie. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . [69] tidyselect_1.0.0. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. R version 4.0.1 (2020-06-06) [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: I've copied the output below in case it helps with troubleshooting. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Try again and choose No. Well occasionally send you account related emails. "4.2") and enter: For older versions of R, please refer to the appropriate 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. data . there is no package called data.table [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Thanks for contributing an answer to Stack Overflow! The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Thanks for contributing an answer to Bioinformatics Stack Exchange! 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 Running. Is the God of a monotheism necessarily omnipotent? Following successful installation of backports BiocManager::install ("DESeq2") will succeed under I am running a new install of R (3.5.0) and RStudio (1.1.414). I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Is there anything I can do to speed it up? Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib 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'. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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). 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. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. Sign in No error messages are returned. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. running multiple versions of the same package, keeping separate libraries for some projects). (Factorization). Is a PhD visitor considered as a visiting scholar? 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 can download DESeq2 using, User Agreement and Privacy It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages I'm having a similar error, but different package: library("DESeq2") Also make sure that you have RTools.exe installed and working. When you load the package, you can observe this error. package rlang was built under R version 3.5.1. 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. What is the output of. . In install.packages() : Warning: cannot remove prior installation of package xfun LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Running under: macOS Catalina 10.15.3, Matrix products: default Is there a proper earth ground point in this switch box? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Making statements based on opinion; back them up with references or personal experience. Traffic: 307 users visited in the last hour, I am new to all this! 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. Platform: x86_64-w64-mingw32/x64 (64-bit) Making statements based on opinion; back them up with references or personal experience. Are you sure the R you're running from the command line is installed through Anaconda as well? call: dots_list() [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 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. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Start R to confirm they are gone. [5] IRanges_2.8.1 S4Vectors_0.12.1 "After the incident", I started to be more careful not to trip over things. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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 I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Is there a proper earth ground point in this switch box? [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Please try the following steps: Quit all R/Rstudio sessions. Acidity of alcohols and basicity of amines. Just updated my previous R to 4.01 and now I cant load DESeq2. Use this. To learn more, see our tips on writing great answers. Installing package(s) 'htmlTable', 'xfun' Policy. Choose Yes. Replacing broken pins/legs on a DIP IC package. Any suggestions would be greatly appreciated. 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': 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. 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? [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: package xfun successfully unpacked and MD5 sums checked 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 You are doing something very wrong when installing your packages. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 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. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 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"). How to notate a grace note at the start of a bar with lilypond? [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 nnet, spatial, survival 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. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Content type 'application/zip' length 233860 bytes (228 KB) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. What am I doing wrong here in the PlotLegends specification? When you load the package, you can observe this error. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Old packages: 'RcppArmadillo', 'survival' [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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: in your system, start R and enter: Follow Use of this site constitutes acceptance of our User Agreement and Privacy library(DESeq2) [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Installing package(s) 'GenomeInfoDbData' requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Already on GitHub? [R] Error: package or namespace load failed for 'ggplot2' in 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]]): By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 R version 3.6.3 (2020-02-29) rev2023.3.3.43278. 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). 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. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Making statements based on opinion; back them up with references or personal experience. Why is this sentence from The Great Gatsby grammatical? R| - (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 . - the incident has nothing to do with me; can I use this this way? downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. binary source needs_compilation How to use Slater Type Orbitals as a basis functions in matrix method correctly? Disconnect between goals and daily tasksIs it me, or the industry? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' I would like to install DESeq2 for DE analysis. 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: Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 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 . How can we prove that the supernatural or paranormal doesn't exist? [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 March 1, 2023, 4:56pm 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: 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. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 If you have a query related to it or one of the replies, start a new topic and refer back with a link. @artembus Sounds like it was a ton of work! Press CTRL-C to abort. - the incident has nothing to do with me; can I use this this way? 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 If you preorder a special airline meal (e.g. 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. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Feedback More info about Internet Explorer and Microsoft Edge. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 March 1, 2023, 3:25pm I was assuming that to be the case. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 I tried following the instructions for 2019.7 as well and I am getting the same error. 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"). Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' This includes any installed libraries. Does a summoned creature play immediately after being summoned by a ready action? I highly recommend that any R/RStudio version not installed inside conda be removed. 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. rstudio - Error: package or namespace load failed for 'tidyverse 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. C:\R\R-3.4.3\library). Use of this site constitutes acceptance of our User Agreement and Privacy guide. 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 Documentation [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Hello, [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. This topic was automatically closed 21 days after the last reply. + "htmlTable", "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. Language(R, Python, SQL) Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Can't Load R DESeq2 Library, Installed All Missing Packages and Still It is working now. 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. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Install DESeq2 through anaconda - Bioinformatics Stack Exchange [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. install.packages("BiocManager"), I get this error: If it fails, required operating system facilities are missing. Warning message: Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Also note, however, that the error you got has been associated in the past with mirror outages. Loading required package: GenomicRanges Looking for incompatible packages.This can take several minutes. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Statistics ; Algorithm(ML, DL,.) Content type 'application/zip' length 386703 bytes (377 KB) Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Not the answer you're looking for? 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. Just realize that I need to write the script "library("DESeq2")" before I proceed. Not the answer you're looking for? Are there tables of wastage rates for different fruit and veg? Thanks for your suggestion. Why is there a voltage on my HDMI and coaxial cables? Fortunately I was able to solve it by doing things from several suggested solutions. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Platform: x86_64-apple-darwin15.6.0 (64-bit) Is there anyone the same as mine error while loading library(DESeq2)? Let me confer with the team. Policy. Loading required package: GenomeInfoDb Glad everything is finally working now. ERROR: lazy loading failed for package Hmisc .onLoad failed in loadNamespace() for 'rlang', details: 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. That plugin is has not been updated to work with later releases of QIIME 2. Remember to always click on the red Show me the content on this page notice when navigating these older versions. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 I need help installing a package "DESeq2" having - RStudio Community there is no package called locfit. package in your R session. 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. Looking for incompatible packages. Citation (from within R, Do I need a thermal expansion tank if I already have a pressure tank? To view documentation for the version of this package installed [7] edgeR_3.16.5 limma_3.30.12 library (olsrr) - Error - General - RStudio Community Follow Up: struct sockaddr storage initialization by network format-string. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 This article explains how to resolve the package or namespace loading error. 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. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Finally After 3-4 manual installations of missing packages everything worked. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Whats the grammar of "For those whose stories they are"? Error when installing Aldex2 - Community Plugin Support - Open Source sessionInfo() Use MathJax to format equations. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 When an R package depends on a newer package version, the required package is downloaded but not loaded. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Why are physically impossible and logically impossible concepts considered separate in terms of probability? Why do academics stay as adjuncts for years rather than move around? You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Open Source Biology & Genetics Interest Group. library(caret) namespace load failed Object sigma not Policy. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. privacy statement. Give up and run everything from the "permitted" library location (e.g. error: object 'rlang_dots_list' not found Policy.

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