call: dots_list() Use of this site constitutes acceptance of our User Agreement and Privacy [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Try again and choose No. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. 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. Policy. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Retrying with flexible solve.Solving environment: Found conflicts! Glad everything is finally working now. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. nnet, spatial, survival [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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!). [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: @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. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Please try the following steps: Quit all R/Rstudio sessions. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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. After 3-4 manual installs everything worked. Post questions about Bioconductor trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: If you try loading the DEseq2 library now, that might work. Policy. Policy. rev2023.3.3.43278. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. install.packages('
', repo='http://nbcgib.uesc.br/mirrors/cran/'). Any suggestions would be greatly appreciated. library(caret) namespace load failed Object sigma not found caret , . If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Learn more about Stack Overflow the company, and our products. install.packages ("zip") We've tried this - and can replicate this issue on a completely new install with no existing package installs. Solving environment: Found conflicts! [7] datasets methods base, other attached packages: Let me confer with the team. 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. I highly recommend that any R/RStudio version not installed inside conda be removed. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 R version 4.0.1 (2020-06-06) Sounds like you might have an issue with which R Rstudio is running. Thanks for your suggestion. Why is this sentence from The Great Gatsby grammatical? ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. package xfun successfully unpacked and MD5 sums checked Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Is there anything I can do to speed it up? there is no package called GenomeInfoDbData I have tried your suggestion and also updating the packages that command indicates. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages MathJax reference. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. I then launched the R application (from the finder, not RStudio) and installed BiocManager. So if you still get this error try changing your CRAN mirror. This can take several minutes. Surly Straggler vs. other types of steel frames. 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 Use MathJax to format equations. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Please read the posting Loading required package: GenomeInfoDb It only takes a minute to sign up. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [a/s/n]: Making statements based on opinion; back them up with references or personal experience. 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: Use this. Start R to confirm they are gone. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Connect and share knowledge within a single location that is structured and easy to search. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Also note, however, that the error you got has been associated in the past with mirror outages. Acidity of alcohols and basicity of amines. Remember to always click on the red Show me the content on this page notice when navigating these older versions. 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. 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"). .onLoad failed in loadNamespace() for 'rlang', details: [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 The error states that the current version is 0.4.5 but 0.4.10 is required. 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. I need help installing a package "DESeq2" having - RStudio Community Bioconductor release. Installation instructions to use this "htmlTable", "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. How do I align things in the following tabular environment? Use of this site constitutes acceptance of our User Agreement and Privacy March 1, 2023, 8:52pm Then I reinstalled R then Rstudio then RTools. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 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. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Policy. 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 . When an R package depends on a newer package version, the required package is downloaded but not loaded. To view documentation for the version of this package installed 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. Not the answer you're looking for? Installing package(s) 'htmlTable', 'xfun' [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Then I reinstalled R then Rstudio then RTools. [13] ggplot23.3.0 car3.0-7 carData3.0-3 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. guide. 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. To learn more, see our tips on writing great answers. [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. Why do academics stay as adjuncts for years rather than move around? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? When you load the package, you can observe this error. Warning message: By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. I also tried something I found on google: but the installation had errors too, I can write them here if needed. 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. 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 In file.copy(savedcopy, lib, recursive = TRUE) : Platform: x86_64-w64-mingw32/x64 (64-bit) May I know is there any other approach I can try? A place where magic is studied and practiced? /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so More info about Internet Explorer and Microsoft Edge. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Any other suggestion? check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Please remember to confirm an answer once you've received one. 9. I do know that it works well in qiime2-2020.6. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) March 1, 2023, 4:56pm Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) In install.packages() : By clicking Sign up for GitHub, you agree to our terms of service and 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 Thank you @hharder. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Find centralized, trusted content and collaborate around the technologies you use most. Error: package GenomeInfoDb could not be loaded. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 package in your R session. I tried to download the "locfit" package but I can't find it anywhere. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 I even tried BiocManager::install("XML") but all failed as shown below. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. R version 3.6.3 (2020-02-29) 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. I just figured Id ask. I hope you can see something I can't see and help me solving this issue. Thanks for contributing an answer to Bioinformatics Stack Exchange! To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Installing package(s) 'XML' Bad: conda install -c bioconda bioconductor-deseq2. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Follow Up: struct sockaddr storage initialization by network format-string. Well occasionally send you account related emails. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Sign in [5] IRanges_2.8.1 S4Vectors_0.12.1 I'm trying to reproduce your problem, so being as precise as possible is important. 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. 1. library ("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 'Hmisc' Installing Hmisc as suggested above did not solve the issue. Documentation [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! 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. :), BiocManager::install("locift") there is no package called Hmisc. Error when installing Aldex2 - Community Plugin Support - Open Source Running under: macOS Catalina 10.15.3, Matrix products: default (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 . Install DESeq2 through anaconda - Bioinformatics Stack Exchange requires R 4 and running more than a couple of releases behind in R risks multiplying problems. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. @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. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR That plugin is has not been updated to work with later releases of QIIME 2. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Also make sure that you have RTools.exe installed and working. Is there a proper earth ground point in this switch box? installation of package GenomeInfoDbData had non-zero exit status. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Thanks for contributing an answer to Stack Overflow! Thanks! DESeq2 - I can't get the library to load - Bioconductor Is there a single-word adjective for "having exceptionally strong moral principles"? 2. Error: package or namespace load failed for 'DESeq2 - Bioconductor [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 I am running a new install of R (3.5.0) and RStudio (1.1.414). While a notebook is attached to a cluster, the R namespace cannot be refreshed. The best answers are voted up and rise to the top, Not the answer you're looking for? sessionInfo() If you preorder a special airline meal (e.g. Asking for help, clarification, or responding to other answers. Disconnect between goals and daily tasksIs it me, or the industry? [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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. Why is there a voltage on my HDMI and coaxial cables? When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. 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 . [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( rstudio - Error: package or namespace load failed for 'tidyverse Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. I was assuming that to be the case. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. so I would try to use BiocManager::install("XML"). If you have a query related to it or one of the replies, start a new topic and refer back with a link. I tried following the instructions for 2019.7 as well and I am getting the same error. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Do I need a thermal expansion tank if I already have a pressure tank? 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. Join us at CRISPR workshops in Koper, Slovenia in 2023. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 DESeq2 installation in R - Bioconductor data . March 1, 2023, 3:25pm Find centralized, trusted content and collaborate around the technologies you use most. Is there a proper earth ground point in this switch box? Making statements based on opinion; back them up with references or personal experience. @artembus Sounds like it was a ton of work! DESeq2: Error: package or namespace load failed for 'DESeq2': objects The package has place the R version constraint. [R] Error: package or namespace load failed for 'ggplot2' in [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 How do you ensure that a red herring doesn't violate Chekhov's gun? But I guess you have many problems with your installation, and I'd suggest. The other option is to download and older version of locfit from the package archive and install manually. Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Running under: macOS Sierra 10.12.3, locale: Platform: x86_64-apple-darwin13.4.0 (64-bit) I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Just realize that I need to write the script "library("DESeq2")" before I proceed. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): library (olsrr) - Error - General - RStudio Community [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 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. Whats the grammar of "For those whose stories they are"? 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. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Why do academics stay as adjuncts for years rather than move around? im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Making statements based on opinion; back them up with references or personal experience. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Hello, The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. It is working now. 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.