It only takes a minute to sign up. Just to add on -- do you require an old version of Bioconductor for your current project? Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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. Running under: macOS Sierra 10.12.3, locale: Old packages: 'RcppArmadillo', 'survival' Warning message: One solution is to find all available packages. March 1, 2023, 3:25pm Join us at CRISPR workshops in Koper, Slovenia in 2023. privacy statement. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Policy. Connect and share knowledge within a single location that is structured and easy to search. 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'. In install.packages() : trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' (Factorization). A place where magic is studied and practiced? 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. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? 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. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8, attached base packages: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Have a question about this project? Installing package(s) 'GenomeInfoDbData' in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 If you preorder a special airline meal (e.g. [7] edgeR_3.16.5 limma_3.30.12 [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 I would recommend installing an older version of QIIME 2 for this plugin to work. [5] IRanges_2.8.1 S4Vectors_0.12.1 9. 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 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Why is there a voltage on my HDMI and coaxial cables? - the incident has nothing to do with me; can I use this this way? [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Making statements based on opinion; back them up with references or personal experience. How to use Slater Type Orbitals as a basis functions in matrix method correctly? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Hello, The package has place the R version constraint. I was assuming that to be the case. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc March 1, 2023, 7:31pm In file.copy(savedcopy, lib, recursive = TRUE) : [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): The best answers are voted up and rise to the top, Not the answer you're looking for? in your system, start R and enter: Follow 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. and then updating the packages that command indicates. From the console install.packages ("rlang") should fix this. Why is this sentence from The Great Gatsby grammatical? C:\R\R-3.4.3\library). package xfun 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. Bioconductor release. Give up and run everything from the "permitted" library location (e.g. I thought that working in a new environment would help, but it didnt. Let me confer with the team. 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. Replacing broken pins/legs on a DIP IC package. Not the answer you're looking for? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. 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 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. 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]]): 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") Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Use of this site constitutes acceptance of our User Agreement and Privacy [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. But I guess you have many problems with your installation, and I'd suggest. Sorry, I'm newbie. Are there tables of wastage rates for different fruit and veg? nnet, spatial, survival. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Thanks for contributing an answer to Stack Overflow! Any other suggestion? It is working now. Is the God of a monotheism necessarily omnipotent? Use of this site constitutes acceptance of our User Agreement and Privacy Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). + ), update = TRUE, ask = FALSE) 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. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 I can download DESeq2 using, User Agreement and Privacy Already on GitHub? Press CTRL-C to abort. 1. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. I highly recommend that any R/RStudio version not installed inside conda be removed. This can take several minutes. I've copied the output below in case it helps with troubleshooting. Use MathJax to format equations. This topic was automatically closed 21 days after the last reply. Well occasionally send you account related emails. To add to this, I have also been using DESeq2 recently and ran into the same problem. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 nnet, spatial, survival [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 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: When you load the package, you can observe this error. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Looking for incompatible packages.This can take several minutes. In addition: Warning message: When you load the package, you can observe this error. Please try reinstalling rlang on a fresh session. Convince your IT department to relax the permissions for R packages Running under: macOS Sierra 10.12.6. Sounds like there might be an issue with conda setup? The other option is to download and older version of locfit from the package archive and install manually. 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: How can we prove that the supernatural or paranormal doesn't exist? Why do academics stay as adjuncts for years rather than move around? Then I reinstalled R then Rstudio then RTools. if (!require("BiocManager", quietly = TRUE)) Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Platform: x86_64-w64-mingw32/x64 (64-bit) 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 do I align things in the following tabular environment? Installing package(s) 'XML' [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 March 1, 2023, 4:56pm [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Choose Yes. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Platform: x86_64-apple-darwin13.4.0 (64-bit) @artembus Sounds like it was a ton of work! Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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"). Looking for incompatible packages. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. .onLoad failed in loadNamespace() for 'rlang', details: Connect and share knowledge within a single location that is structured and easy to search. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. What am I doing wrong here in the PlotLegends specification? Is there a proper earth ground point in this switch box? Installation instructions to use this ERROR: dependency Hmisc is not available for package DESeq2 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Not the answer you're looking for? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 4. I also tried something I found on google: but the installation had errors too, I can write them here if needed. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Please try the following steps: Quit all R/Rstudio sessions. Sounds like you might have an issue with which R Rstudio is running. R version 4.0.1 (2020-06-06) If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : So, supposedly the issue is with Hmisc. 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? What is the output of. 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. Any suggestions would be greatly appreciated. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: enter citation("DESeq2")): To install this package, start R (version 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. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Learn more about Stack Overflow the company, and our products. Is there a single-word adjective for "having exceptionally strong moral principles"? Do I need a thermal expansion tank if I already have a pressure tank? [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: 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 '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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) If it fails, required operating system facilities are missing. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 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. Why do many companies reject expired SSL certificates as bugs in bug bounties? Styling contours by colour and by line thickness in QGIS. I guess that means we can finally close this issue. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) No error messages are returned. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Are you sure the R you're running from the command line is installed through Anaconda as well? We've tried this - and can replicate this issue on a completely new install with no existing package installs. Policy. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 I tried to download the "locfit" package but I can't find it anywhere. guide. 2. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Thank you @hharder. To resolve this error, install the required package as a cluster-installed library. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Acidity of alcohols and basicity of amines. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 [16] phyloseq1.30.0, loaded via a namespace (and not attached): Running under: macOS Catalina 10.15.3, Matrix products: default 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. 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 . Connect and share knowledge within a single location that is structured and easy to search. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. there is no package called data.table 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. rev2023.3.3.43278. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Thanks for your suggestion. As such there are two solutions that may be more or less attainable given your own IT system. To learn more, see our tips on writing great answers. Open Source Biology & Genetics Interest Group. Loading required package: GenomeInfoDb 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 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. 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. Feedback [7] datasets methods base, other attached packages: [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 running multiple versions of the same package, keeping separate libraries for some projects). 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. After 3-4 manual installs everything worked. error: object 'rlang_dots_list' not found Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Installing package(s) 'htmlTable', 'xfun' Please read the posting [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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 Statistics ; Algorithm(ML, DL,.) When an R package depends on a newer package version, the required package is downloaded but not loaded. 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'. 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. That plugin is has not been updated to work with later releases of QIIME 2. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: binary source needs_compilation [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? 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 tried again and again was met with missing packages BUT!!! I have tried your suggestion and also updating the packages that command indicates. Is a PhD visitor considered as a visiting scholar? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked install.packages("BiocManager"), I get this error: [13] ggplot23.3.0 car3.0-7 carData3.0-3 Use this. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. [1] stats4 parallel stats graphics grDevices utils /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Platform: x86_64-apple-darwin17.0 (64-bit) RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 [69] tidyselect_1.0.0. [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. Asking for help, clarification, or responding to other answers. Should I update the Bioconductor to latest version instead? Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. 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. You signed in with another tab or window. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 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. there is no package called GenomeInfoDbData Thanks! + "htmlTable", "xfun" downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Finally After 3-4 manual installations of missing packages everything worked. To learn more, see our tips on writing great answers. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Language(R, Python, SQL) I'm trying to reproduce your problem, so being as precise as possible is important. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. By clicking Sign up for GitHub, you agree to our terms of service and This article explains how to resolve the package or namespace loading error. Retrying with flexible solve.Solving environment: Found conflicts! 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]]):
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