error: package or namespace load failed for 'deseq2

I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Installing Hmisc as suggested above did not solve the issue. This topic was automatically closed 21 days after the last reply. Bioconductor release. Find centralized, trusted content and collaborate around the technologies you use most. What am I doing wrong here in the PlotLegends specification? Use of this site constitutes acceptance of our User Agreement and Privacy there is no package called locfit. library(caret) namespace load failed Object sigma not found caret , . Use of this site constitutes acceptance of our User Agreement and Privacy Running under: macOS Sierra 10.12.3, locale: rev2023.3.3.43278. R DESeq2 - 4. Thanks! - the incident has nothing to do with me; can I use this this way? This article explains how to resolve the package or namespace loading error. 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. The other option is to download and older version of locfit from the package archive and install manually. 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 . This includes any installed libraries. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 [5] IRanges_2.8.1 S4Vectors_0.12.1 Not the answer you're looking for? [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 @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. Sorry, I'm newbie. Remember to always click on the red Show me the content on this page notice when navigating these older versions. You signed in with another tab or window. Installing package(s) 'htmlTable', 'xfun' What is a word for the arcane equivalent of a monastery? From the console install.packages ("rlang") should fix this. Is there a single-word adjective for "having exceptionally strong moral principles"? binary source needs_compilation Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? to your account. Solution To resolve this error, install the required package as a cluster-installed library. Does a summoned creature play immediately after being summoned by a ready action? MathJax reference. 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. 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") rstudio - Error: package or namespace load failed for 'tidyverse [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 We've tried this - and can replicate this issue on a completely new install with no existing package installs. a, There are binary versions available but the source versions are later: [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: I do know that it works well in qiime2-2020.6. Give up and run everything from the "permitted" library location (e.g. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Use of this site constitutes acceptance of our User Agreement and Privacy R| - Retrying with flexible solve.Solving environment: Found conflicts! Making statements based on opinion; back them up with references or personal experience. Content type 'application/zip' length 4255589 bytes (4.1 MB) [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 If you try loading the DEseq2 library now, that might work. rev2023.3.3.43278. Looking for incompatible packages.This can take several minutes. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Replacing broken pins/legs on a DIP IC package. And finally, install the problem packages, perhaps also DESeq2. Policy. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext requires R 4 and running more than a couple of releases behind in R risks multiplying problems. If you have a query related to it or one of the replies, start a new topic and refer back with a link. Running. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' I even tried BiocManager::install("XML") but all failed as shown below. I tried following the instructions for 2019.7 as well and I am getting the same error. + ), update = TRUE, ask = FALSE) Error: package GenomeInfoDb could not be loaded. Is a PhD visitor considered as a visiting scholar? if (!require("BiocManager", quietly = TRUE)) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: package rlang was built under R version 3.5.1. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Asking for help, clarification, or responding to other answers. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat It is working now. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: I was assuming that to be the case. 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 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. 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. 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. Connect and share knowledge within a single location that is structured and easy to search. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Policy. 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. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. 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. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. How do you ensure that a red herring doesn't violate Chekhov's gun? Looking for incompatible packages. vegan) just to try it, does this inconvenience the caterers and staff? 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"). Sounds like there might be an issue with conda setup? Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Fortunately I was able to solve it by doing things from several suggested solutions. C:\R\R-3.4.3\library). What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Is there anyone the same as mine error while loading library(DESeq2)? I would like to install DESeq2 for DE analysis. Thanks for your suggestion. I just figured Id ask. Platform: x86_64-apple-darwin13.4.0 (64-bit) [a/s/n]: 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 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. there is no package called GenomeInfoDbData Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Install DESeq2 through anaconda - Bioinformatics Stack Exchange Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. ERROR: dependency Hmisc is not available for package DESeq2 Loading required package: GenomeInfoDb I have tried your suggestion and also updating the packages that command indicates. and then updating the packages that command indicates. Why do academics stay as adjuncts for years rather than move around? [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Have a question about this project? When you load the package, you can observe this error. Rload failed - But I guess you have many problems with your installation, and I'd suggest. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? (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 . * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc I installed the package successfully with conda, but Rstudio is apparently does not know about it. [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. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Try again and choose No. Are there tables of wastage rates for different fruit and veg? I can download DESeq2 using, User Agreement and Privacy 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. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 @KonradRudolph It's pacman (not packman) and you are correct in that it's basically just a wrapper for, Thanks for your suggestion, I tried doing this step by step as you said but the biocLite command still did throw errors for missing packages. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Surly Straggler vs. other types of steel frames. Sign in Any other suggestion? Policy. ()library(DESeq2):Error in loadNamespace: no package called ""s Not the answer you're looking for? in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so DESeq2 - I can't get the library to load - Bioconductor [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. 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. 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. sessionInfo() [7] datasets methods base, other attached packages: ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 If not fixed, Try removing remove.packages (rlang) then. Just updated my previous R to 4.01 and now I cant load DESeq2. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Installing package(s) 'XML' How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Content type 'application/zip' length 233860 bytes (228 KB) So, supposedly the issue is with Hmisc. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Surly Straggler vs. other types of steel frames. Connect and share knowledge within a single location that is structured and easy to search. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR In addition: Warning message: enter citation("DESeq2")): To install this package, start R (version 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). R version 3.6.3 (2020-02-29) sessionInfo() (Factorization). Thanks for contributing an answer to Bioinformatics Stack Exchange! Are you sure the R you're running from the command line is installed through Anaconda as well? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Why is there a voltage on my HDMI and coaxial cables? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Is there a proper earth ground point in this switch box? The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' "After the incident", I started to be more careful not to trip over things. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 guide. Then I reinstalled R then Rstudio then RTools. [16] phyloseq1.30.0, loaded via a namespace (and not attached): biocLite(), install.packages() (and the devtools equivalent?) 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. "After the incident", I started to be more careful not to trip over things. 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. 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. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Running under: macOS Catalina 10.15.3, Matrix products: default Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. data . [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: When you load the package, you can observe this error. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 rev2023.3.3.43278. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. March 1, 2023, 3:25pm Is the God of a monotheism necessarily omnipotent? [69] tidyselect_1.0.0. Is a PhD visitor considered as a visiting scholar? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. it would be good to hear any speculation you have of how this might have happened). package in your R session. 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: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): To learn more, see our tips on writing great answers. Platform: x86_64-w64-mingw32/x64 (64-bit) Try installing zip, and then loading olsrr. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. to allow custom library locations. . Error: package or namespace load failed, object not found Is there anything I can do to speed it up? The error states that the current version is 0.4.5 but 0.4.10 is required. Use this. Loading required package: GenomicRanges Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so How can I fix error with loading package in R ? | ResearchGate Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) A place where magic is studied and practiced? To view documentation for the version of this package installed 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. No error messages are returned. Does anyone know why I'm getting the following message when I load tidyverse in a new session. 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 resolve this error, install the required package as a cluster-installed library. When an R package depends on a newer package version, the required package is downloaded but not loaded. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 After 3-4 manual installs everything worked. 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. :), BiocManager::install("locift") [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Then I reinstalled R then Rstudio then RTools. 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"). trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 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. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Warning: cannot remove prior installation of package xfun library (olsrr) - Error - General - RStudio Community 2. Find centralized, trusted content and collaborate around the technologies you use most. Finally After 3-4 manual installations of missing packages everything worked. 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. 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).

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