The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. I highly recommend that any R/RStudio version not installed inside conda be removed. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 How do you ensure that a red herring doesn't violate Chekhov's gun? there is no package called Hmisc. 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"). Hello, package rlang was built under R version 3.5.1. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Choose Yes. Please try reinstalling rlang on a fresh session. Policy. Use this. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Error: package GenomeInfoDb could not be loaded. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Warning: cannot remove prior installation of package xfun check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Does anyone know why I'm getting the following message when I load tidyverse in a new 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, 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 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? 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. 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: A place where magic is studied and practiced? R version 4.0.1 (2020-06-06) Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. When an R package depends on a newer package version, the required package is downloaded but not loaded. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. DESeq2_2301_76497647-CSDN 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. Whats the grammar of "For those whose stories they are"? Running under: macOS Catalina 10.15.3, Matrix products: default We've tried this - and can replicate this issue on a completely new install with no existing package installs. While a notebook is attached to a cluster, the R namespace cannot be refreshed. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Surly Straggler vs. other types of steel frames. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 but when I go to load the libraries I get this error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : Please remember to confirm an answer once you've received one. Find centralized, trusted content and collaborate around the technologies you use most. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Styling contours by colour and by line thickness in QGIS. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? [1] stats4 parallel stats graphics grDevices utils Is there a proper earth ground point in this switch box? /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages I also tried something I found on google: but the installation had errors too, I can write them here if needed. Post questions about Bioconductor LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open I even tried BiocManager::install("XML") but all failed as shown below. Platform: x86_64-apple-darwin15.6.0 (64-bit) error: object 'rlang_dots_list' not found [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 MathJax reference. May I know is there any other approach I can try? I've copied the output below in case it helps with troubleshooting. The best answers are voted up and rise to the top, Not the answer you're looking for? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Also make sure that you have RTools.exe installed and working. 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 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Update all/some/none? Erasmus+ funds available! My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? package xfun successfully unpacked and MD5 sums checked 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. Have a question about this project? [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 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. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 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. Solving environment: Found conflicts! 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. Then I reinstalled R then Rstudio then RTools. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Why is this sentence from The Great Gatsby grammatical? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Start R to confirm they are gone. now when I tried installing the missing packages they did install. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. [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. Policy. If not fixed, Try removing remove.packages (rlang) then. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. - the incident has nothing to do with me; can I use this this way? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Sounds like you might have an issue with which R Rstudio is running. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. 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. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 And finally, install the problem packages, perhaps also DESeq2. 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. How can I fix error with loading package in R ? | ResearchGate "htmlTable", "xfun" [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Should I update the Bioconductor to latest version instead? 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. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Connect and share knowledge within a single location that is structured and easy to search. to allow custom library locations. Citation (from within R, enter citation ("DESeq2") ): Installation To install this package, start R (version "4.2") and enter: if (!require ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install ("DESeq2") For older versions of R, please refer to the appropriate Bioconductor release . C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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 Error when installing Aldex2 - Community Plugin Support - Open Source C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. [16] phyloseq1.30.0, loaded via a namespace (and not attached): Any suggestions would be greatly appreciated. Are there tables of wastage rates for different fruit and veg? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Platform: x86_64-apple-darwin17.0 (64-bit) Policy. Resolving package or namespace loading error To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Does a summoned creature play immediately after being summoned by a ready action? [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 sessionInfo() Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? If you try loading the DEseq2 library now, that might work. 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 there is no package called locfit. Thank you @hharder. Sorry, I'm newbie. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Well occasionally send you account related emails. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Making statements based on opinion; back them up with references or personal experience. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Do I need a thermal expansion tank if I already have a pressure tank? Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Finally After 3-4 manual installations of missing packages everything worked. Asking for help, clarification, or responding to other answers. Is a PhD visitor considered as a visiting scholar? I thought that working in a new environment would help, but it didnt. Making statements based on opinion; back them up with references or personal experience. So if you still get this error try changing your CRAN mirror. 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). Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Have you tried install.packages("locfit") ? Also note, however, that the error you got has been associated in the past with mirror outages. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Installing package(s) 'XML' [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 R version 3.6.3 (2020-02-29) Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib I can download DESeq2 using, User Agreement and Privacy Installing package(s) 'GenomeInfoDbData' [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. 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. install.packages("BiocManager"), I get this error: I just figured Id ask. 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 have a query related to it or one of the replies, start a new topic and refer back with a link. Whats the grammar of "For those whose stories they are"? Disconnect between goals and daily tasksIs it me, or the industry? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide, You can try installing packages in R (which comes with R 3.5.1, not RStudio). @artembus Sounds like it was a ton of work! To resolve this error, install the required package as a cluster-installed library. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Can't Load R DESeq2 Library, Installed All Missing Packages and Still Installing Hmisc as suggested above did not solve the issue. Loading required package: GenomeInfoDb binary source needs_compilation [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Just to add on -- do you require an old version of Bioconductor for your current project? This topic was automatically closed 21 days after the last reply. Documentation [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Just updated my previous R to 4.01 and now I cant load DESeq2. to your account. Acidity of alcohols and basicity of amines. Connect and share knowledge within a single location that is structured and easy to search. Please read the posting Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Let me confer with the team. Platform: x86_64-apple-darwin13.4.0 (64-bit) Thanks for contributing an answer to Stack Overflow! It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). The package has place the R version constraint. Bioconductor - DESeq2 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Running under: macOS Sierra 10.12.3, locale: Learn more about Stack Overflow the company, and our products. "4.2") and enter: For older versions of R, please refer to the appropriate To learn more, see our tips on writing great answers. 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. Surly Straggler vs. other types of steel frames. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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. 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. I'm trying to reproduce your problem, so being as precise as possible is important. Running under: Windows 10 x64 (build 18362), locale: To learn more, see our tips on writing great answers. 2. Warning message: Find centralized, trusted content and collaborate around the technologies you use most. 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. . Open Source Biology & Genetics Interest Group. Give up and run everything from the "permitted" library location (e.g. 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. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 When you load the package, you can observe this error. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? library(caret) namespace load failed Object sigma not found caret , . In install.packages() : Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? 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 Sign up for GitHub, you agree to our terms of service and March 1, 2023, 4:56pm 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. Thanks for contributing an answer to Bioinformatics Stack Exchange! Why do academics stay as adjuncts for years rather than move around? a, There are binary versions available but the source versions are later: Policy. 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. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 "After the incident", I started to be more careful not to trip over things. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. @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.