Finally After 3-4 manual installations of missing packages everything worked. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). This article explains how to resolve the package or namespace loading error. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Policy. Why is this sentence from The Great Gatsby grammatical? 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: Also make sure that you have RTools.exe installed and working. Installing package(s) 'htmlTable', 'xfun' Are you sure the R you're running from the command line is installed through Anaconda as well? Sounds like there might be an issue with conda setup? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? How do I align things in the following tabular environment? - the incident has nothing to do with me; can I use this this way? Is there a single-word adjective for "having exceptionally strong moral principles"? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Content type 'application/zip' length 233860 bytes (228 KB) [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Warning: cannot remove prior installation of package xfun How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. Looking for incompatible packages.This can take several minutes. Running under: Windows 10 x64 (build 18362), locale: 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. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 May be the version has problem How can I do ? rev2023.3.3.43278. Policy. Statistics ; Algorithm(ML, DL,.) 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]]): Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Also note, however, that the error you got has been associated in the past with mirror outages. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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 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. [7] edgeR_3.16.5 limma_3.30.12 [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Please remember to confirm an answer once you've received one. guide. package in your R session. Asking for help, clarification, or responding to other answers. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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. Why do academics stay as adjuncts for years rather than move around? Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? This includes any installed libraries. Please try reinstalling rlang on a fresh session. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'XML' so I would try to use BiocManager::install ("XML"). Sounds like you might have an issue with which R Rstudio is running. [16] phyloseq1.30.0, loaded via a namespace (and not attached): Replacing broken pins/legs on a DIP IC package. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) What am I doing wrong here in the PlotLegends specification? 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. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Whats the grammar of "For those whose stories they are"? Connect and share knowledge within a single location that is structured and easy to search. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 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 . check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Try installing zip, and then loading olsrr. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Remember to always click on the red Show me the content on this page notice when navigating these older versions. Fortunately I was able to solve it by doing things from several suggested solutions. No error messages are returned. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) there is no package called Hmisc. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Is there anyone the same as mine error while loading library(DESeq2)? 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: Start R to confirm they are gone. Thanks for contributing an answer to Bioinformatics Stack Exchange! I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. 4. R version 3.6.3 (2020-02-29) Installation instructions to use this trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' to allow custom library locations. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. It only takes a minute to sign up. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Is there a proper earth ground point in this switch box? The package has place the R version constraint. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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. [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. 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. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. installation of package GenomeInfoDbData had non-zero exit status. Convince your IT department to relax the permissions for R packages running multiple versions of the same package, keeping separate libraries for some projects). Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Content type 'application/zip' length 4255589 bytes (4.1 MB) Platform: x86_64-w64-mingw32/x64 (64-bit) "htmlTable", "xfun" [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 error: object 'rlang_dots_list' not found [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 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. Warning message: What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? March 1, 2023, 8:52pm What do I need to do to reproduce your problem? It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. if (!require("BiocManager", quietly = TRUE)) From the console install.packages ("rlang") should fix this. Update all/some/none? I just figured Id ask. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 I would recommend installing an older version of QIIME 2 for this plugin to work. so I would try to use BiocManager::install("XML"). Disconnect between goals and daily tasksIs it me, or the industry? Find centralized, trusted content and collaborate around the technologies you use most. @artembus Sounds like it was a ton of work! nnet, spatial, survival. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 When an R package depends on a newer package version, the required package is downloaded but not loaded. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). A place where magic is studied and practiced? . 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? enter citation("DESeq2")): To install this package, start R (version Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) So if you still get this error try changing your CRAN mirror. 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 Loading required package: GenomeInfoDb (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 . rev2023.3.3.43278. Then I reinstalled R then Rstudio then RTools. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. March 1, 2023, 4:56pm Find centralized, trusted content and collaborate around the technologies you use most. To resolve this error, install the required package as a cluster-installed library. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Are there tables of wastage rates for different fruit and veg? [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. Policy. Policy. Solving environment: Found conflicts! Choose Yes. Asking for help, clarification, or responding to other answers. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Running. In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. Whats the grammar of "For those whose stories they are"? 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 If not fixed, Try removing remove.packages (rlang) then. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' In file.copy(savedcopy, lib, recursive = TRUE) : 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. 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'. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. After 3-4 manual installs everything worked. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Have you tried install.packages("locfit") ? Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Making statements based on opinion; back them up with references or personal experience. Any suggestions would be greatly appreciated. in your system, start R and enter: Follow nnet, spatial, survival LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Is the God of a monotheism necessarily omnipotent? You signed in with another tab or window. [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: Language(R, Python, SQL) [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 9. By clicking Sign up for GitHub, you agree to our terms of service and [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 I then launched the R application (from the finder, not RStudio) and installed BiocManager. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . 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). [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 [69] tidyselect_1.0.0. Platform: x86_64-apple-darwin13.4.0 (64-bit) Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. 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. 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 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. 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. now when I tried installing the missing packages they did install. Let me confer with the team. Policy. I highly recommend that any R/RStudio version not installed inside conda be removed. Feedback 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. I do know that it works well in qiime2-2020.6. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so + ), update = TRUE, ask = FALSE) [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Is a PhD visitor considered as a visiting scholar? Use of this site constitutes acceptance of our User Agreement and Privacy C:\R\R-3.4.3\library). (Factorization). 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. 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. That plugin is has not been updated to work with later releases of QIIME 2. 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 The best answers are voted up and rise to the top, Not the answer you're looking for? When you load the package, you can observe this error. More info about Internet Explorer and Microsoft Edge. .onLoad failed in loadNamespace() for 'rlang', details: Already on GitHub? You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. 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. How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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. The error states that the current version is 0.4.5 but 0.4.10 is required. You are doing something very wrong when installing your 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. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 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. R version 4.0.1 (2020-06-06) [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Just updated my previous R to 4.01 and now I cant load DESeq2. Thanks for contributing an answer to Stack Overflow! 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. Thanks! Surly Straggler vs. other types of steel frames. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Please read the posting Making statements based on opinion; back them up with references or personal experience. 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"). Solution To resolve this error, install the required package as a cluster-installed library. Installing package(s) 'GenomeInfoDbData' If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. 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"). Citation (from within R, Thanks for your suggestion. Why do many companies reject expired SSL certificates as bugs in bug bounties? [7] datasets methods base, other attached packages: Warning: restored xfun, The downloaded binary packages are in Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") and then updating the packages that command indicates. New replies are no longer allowed. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Is there a proper earth ground point in this switch box? [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Is a PhD visitor considered as a visiting scholar? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Do I need a thermal expansion tank if I already have a pressure tank? 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. Running under: macOS Sierra 10.12.3, locale: Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. 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]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 I was assuming that to be the case. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, I even tried BiocManager::install("XML") but all failed as shown below. :), BiocManager::install("locift") I tried following the instructions for 2019.7 as well and I am getting the same error. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 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'. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Any other suggestion? [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 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. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': 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. To learn more, see our tips on writing great answers. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. How to notate a grace note at the start of a bar with lilypond? Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Why do academics stay as adjuncts for years rather than move around? [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: Platform: x86_64-apple-darwin15.6.0 (64-bit) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). a, There are binary versions available but the source versions are later: Connect and share knowledge within a single location that is structured and easy to search. 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.
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