R version 4.0.1 (2020-06-06) Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Find centralized, trusted content and collaborate around the technologies you use most. I even tried BiocManager::install("XML") but all failed as shown below. Statistics ; Algorithm(ML, DL,.) "After the incident", I started to be more careful not to trip over things. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Content type 'application/zip' length 4255589 bytes (4.1 MB) 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. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Platform: x86_64-w64-mingw32/x64 (64-bit) trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 1. 4. 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Use this. 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? Just to add on -- do you require an old version of Bioconductor for your current project? Platform: x86_64-apple-darwin17.0 (64-bit) I thought that working in a new environment would help, but it didnt. Give up and run everything from the "permitted" library location (e.g. If you preorder a special airline meal (e.g. I then launched the R application (from the finder, not RStudio) and installed BiocManager. library(DESeq2) . 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"). What is the output of. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Content type 'application/zip' length 233860 bytes (228 KB) As such there are two solutions that may be more or less attainable given your own IT system. I've copied the output below in case it helps with troubleshooting. Running under: macOS Sierra 10.12.6. How to notate a grace note at the start of a bar with lilypond? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Policy. That plugin is has not been updated to work with later releases of QIIME 2. 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. Press CTRL-C to abort. installation of package GenomeInfoDbData had non-zero exit status. Thank you @hharder. 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). Did you do that? Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Warning: cannot remove prior installation of package xfun By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 there is no package called locfit. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Glad everything is finally working now. Language(R, Python, SQL) 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. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under 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. What am I doing wrong here in the PlotLegends specification? I'm having a similar error, but different package: library("DESeq2") "4.2") and enter: For older versions of R, please refer to the appropriate Follow Up: struct sockaddr storage initialization by network format-string. [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: Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. [7] edgeR_3.16.5 limma_3.30.12 If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. I have tried your suggestion and also updating the packages that command indicates. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 A place where magic is studied and practiced? To add to this, I have also been using DESeq2 recently and ran into the same problem. in your system, start R and enter: Follow How do you ensure that a red herring doesn't violate Chekhov's gun? [a/s/n]: I would recommend installing an older version of QIIME 2 for this plugin to work. We've tried this - and can replicate this issue on a completely new install with no existing package installs. install.packages ("zip") Policy. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Just realize that I need to write the script "library("DESeq2")" before I proceed. Is there a proper earth ground point in this switch box? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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. 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. Open Source Biology & Genetics Interest Group. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Learn more about Stack Overflow the company, and our products. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Is a PhD visitor considered as a visiting scholar? 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). Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 I highly recommend that any R/RStudio version not installed inside conda be removed. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Erasmus+ funds available! I do know that it works well in qiime2-2020.6. But I guess you have many problems with your installation, and I'd suggest. @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. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): rev2023.3.3.43278. Policy. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? New replies are no longer allowed. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat [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: :), BiocManager::install("locift") [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. enter citation("DESeq2")): To install this package, start R (version Why are physically impossible and logically impossible concepts considered separate in terms of probability? Sounds like there might be an issue with conda setup? [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [1] stats4 parallel stats graphics grDevices utils 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. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked To learn more, see our tips on writing great answers. In addition: Warning message: I guess that means we can finally close this issue. 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"). I was assuming that to be the case. May I know is there any other approach I can try? I am running a new install of R (3.5.0) and RStudio (1.1.414). Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. it would be good to hear any speculation you have of how this might have happened). unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': The error states that the current version is 0.4.5 but 0.4.10 is required. and then updating the packages that command indicates. Running under: Windows 10 x64 (build 18362), locale: Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 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. 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: 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 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. Update all/some/none? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Making statements based on opinion; back them up with references or personal experience. Looking for incompatible packages.This can take several minutes. library(DESeq2) 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. Choose Yes. error: object 'rlang_dots_list' not found I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Are you sure the R you're running from the command line is installed through Anaconda as well? Already on GitHub? Should I update the Bioconductor to latest version instead? So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 I also tried something I found on google: but the installation had errors too, I can write them here if needed. 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. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. I can download DESeq2 using, User Agreement and Privacy 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). 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. I just figured Id ask. 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. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Any suggestions would be greatly appreciated. Sign in 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. 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 In install.packages() : 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. 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. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. What do I need to do to reproduce your problem? [5] IRanges_2.8.1 S4Vectors_0.12.1 When you load the package, you can observe this error. now when I tried installing the missing packages they did install. Running under: macOS Sierra 10.12.3, locale: [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 call: dots_list() I installed the package successfully with conda, but Rstudio is apparently does not know about it. I tried again and again was met with missing packages BUT!!! requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? By clicking Sign up for GitHub, you agree to our terms of service and Why do academics stay as adjuncts for years rather than move around? One solution is to find all available packages. Installing package(s) 'XML' Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. I tried to download the "locfit" package but I can't find it anywhere. Finally After 3-4 manual installations of missing packages everything worked. 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. nnet, spatial, survival. C:\R\R-3.4.3\library). there is no package called GenomeInfoDbData To subscribe to this RSS feed, copy and paste this URL into your RSS reader. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Surly Straggler vs. other types of steel frames. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages When an R package depends on a newer package version, the required package is downloaded but not loaded. privacy statement. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Start R to confirm they are gone. 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 . 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 - the incident has nothing to do with me; can I use this this way? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? if (!require("BiocManager", quietly = TRUE)) [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 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. Styling contours by colour and by line thickness in QGIS. 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 It is working now. To view documentation for the version of this package installed Asking for help, clarification, or responding to other answers. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 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. (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 . March 1, 2023, 7:31pm [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Installing package(s) 'htmlTable', 'xfun' to your account. R version 3.6.1 (2019-07-05) You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Is there a proper earth ground point in this switch box? How to use Slater Type Orbitals as a basis functions in matrix method correctly? It only takes a minute to sign up. March 1, 2023, 8:52pm .onLoad failed in loadNamespace() for 'rlang', details: [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Any other suggestion? 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!). Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. "After the incident", I started to be more careful not to trip over things. 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. [13] ggplot23.3.0 car3.0-7 carData3.0-3 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. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Is there anyone the same as mine error while loading library(DESeq2)? Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Making statements based on opinion; back them up with references or personal experience. Why do academics stay as adjuncts for years rather than move around? And finally, install the problem packages, perhaps also DESeq2. While a notebook is attached to a cluster, the R namespace cannot be refreshed. [16] phyloseq1.30.0, loaded via a namespace (and not attached): [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Please remember to confirm an answer once you've received one. Then I reinstalled R then Rstudio then RTools. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Platform: x86_64-apple-darwin15.6.0 (64-bit) Replacing broken pins/legs on a DIP IC package. You are doing something very wrong when installing your packages. Sorry, I'm newbie. 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. Solving environment: Found conflicts! Content type 'application/zip' length 386703 bytes (377 KB) Please read the posting From the console install.packages ("rlang") should fix this. 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. 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. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? To learn more, see our tips on writing great answers. Let me confer with the team. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I tried following the instructions for 2019.7 as well and I am getting the same error. Running. If it fails, required operating system facilities are missing. So, supposedly the issue is with Hmisc. Find centralized, trusted content and collaborate around the technologies you use most. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Running under: macOS Catalina 10.15.3, Matrix products: default Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. This article explains how to resolve the package or namespace loading error. Thanks for your suggestion. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Warning message: Policy. Connect and share knowledge within a single location that is structured and easy to search. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 When you load the package, you can observe this error. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 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'.