Connect and share knowledge within a single location that is structured and easy to search. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Have you tried install.packages("locfit") ? 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. This topic was automatically closed 21 days after the last reply. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. 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. Why do academics stay as adjuncts for years rather than move around? Disconnect between goals and daily tasksIs it me, or the industry? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [a/s/n]: Old packages: 'RcppArmadillo', 'survival' [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Why is there a voltage on my HDMI and coaxial cables? Post questions about Bioconductor [5] IRanges_2.8.1 S4Vectors_0.12.1 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Find centralized, trusted content and collaborate around the technologies you use most. Let me confer with the team. Try again and choose No. DESeq2_2301_76497647-CSDN In file.copy(savedcopy, lib, recursive = TRUE) : [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 there is no package called GenomeInfoDbData Just updated my previous R to 4.01 and now I cant load DESeq2. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Erasmus+ funds available! [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Sorry, I'm newbie. After 3-4 manual installs everything worked. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Not the answer you're looking for? Content type 'application/zip' length 4255589 bytes (4.1 MB) How to use Slater Type Orbitals as a basis functions in matrix method correctly? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Then I reinstalled R then Rstudio then RTools. Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. Thanks for your suggestion. Please read the posting [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: I tried to download the "locfit" package but I can't find it anywhere. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Why are physically impossible and logically impossible concepts considered separate in terms of probability? [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin17.0 (64-bit) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. March 1, 2023, 7:31pm Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Resolving package or namespace loading error https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6: https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip', User Agreement and Privacy [7] datasets methods base, other attached packages: Does a summoned creature play immediately after being summoned by a ready action? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [69] tidyselect_1.0.0. So if you still get this error try changing your CRAN mirror. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc privacy statement. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. How to notate a grace note at the start of a bar with lilypond? Surly Straggler vs. other types of steel frames. there is no package called GenomeInfoDbData [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. Running under: Windows 10 x64 (build 18362), locale: 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: vegan) just to try it, does this inconvenience the caterers and staff? Follow Up: struct sockaddr storage initialization by network format-string. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Press CTRL-C to abort. running multiple versions of the same package, keeping separate libraries for some projects). March 1, 2023, 4:56pm By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 library(caret) namespace load failed Object sigma not found caret , . "htmlTable", "xfun" To subscribe to this RSS feed, copy and paste this URL into your RSS reader. a, There are binary versions available but the source versions are later: Why do many companies reject expired SSL certificates as bugs in bug bounties? [7] edgeR_3.16.5 limma_3.30.12 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 A place where magic is studied and practiced? Surly Straggler vs. other types of steel frames. 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. Styling contours by colour and by line thickness in QGIS. I just figured Id ask. "After the incident", I started to be more careful not to trip over things. Making statements based on opinion; back them up with references or personal experience. 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!!! How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 install.packages ("zip") Please remember to confirm an answer once you've received one. Error when installing Aldex2 - Community Plugin Support - Open Source library(DESeq2) Well occasionally send you account related emails. I've copied the output below in case it helps with troubleshooting. 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]]): 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]]) : May I know is there any other approach I can try? Choose Yes. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Already on GitHub? R version 3.6.3 (2020-02-29) Did you do that? How do I align things in the following tabular environment? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Just realize that I need to write the script "library("DESeq2")" before I proceed. What is the output of. To add to this, I have also been using DESeq2 recently and ran into the same problem. 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? I am running a new install of R (3.5.0) and RStudio (1.1.414). How to use Slater Type Orbitals as a basis functions in matrix method correctly? (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 . Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Why do academics stay as adjuncts for years rather than move around? Platform: x86_64-apple-darwin15.6.0 (64-bit) [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 [R] Error: package or namespace load failed for 'ggplot2' in Are there tables of wastage rates for different fruit and veg? Looking for incompatible packages.This can take several minutes. 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. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Citation (from within R, ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR And finally, install the problem packages, perhaps also DESeq2. March 1, 2023, 3:25pm 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. Not the answer you're looking for? Sounds like there might be an issue with conda setup? 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. there is no package called locfit. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Use of this site constitutes acceptance of our User Agreement and Privacy installation of package GenomeInfoDbData had non-zero exit status. How can we prove that the supernatural or paranormal doesn't exist? I even tried BiocManager::install("XML") but all failed as shown below. Connect and share knowledge within a single location that is structured and easy to search. Running under: macOS Sierra 10.12.6. 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 . Whats the grammar of "For those whose stories they are"? Glad everything is finally working now. May be the version has problem How can I do ? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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: Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext I also tried something I found on google: but the installation had errors too, I can write them here if needed. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Please try the following steps: Quit all R/Rstudio sessions. 9. Is there anything I can do to speed it up? 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. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Policy. Looking for incompatible packages. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Bioconductor - DESeq2 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. To learn more, see our tips on writing great answers. 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[33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 [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: In install.packages() : By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [1] stats4 parallel stats graphics grDevices utils check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: error: object 'rlang_dots_list' not found Use of this site constitutes acceptance of our User Agreement and Privacy ERROR: lazy loading failed for package Hmisc I hope you can see something I can't see and help me solving this issue. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Why is this sentence from The Great Gatsby grammatical? 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). Should I update the Bioconductor to latest version instead? 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. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Is there a single-word adjective for "having exceptionally strong moral principles"? Loading required package: GenomeInfoDb [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 How do you ensure that a red herring doesn't violate Chekhov's gun? [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 It is working now. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 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"). install.packages("BiocManager"), I get this error: 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 . What am I doing wrong here in the PlotLegends specification? To resolve this error, install the required package as a cluster-installed library. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. 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. Replacing broken pins/legs on a DIP IC package. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 [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: Thanks for contributing an answer to Bioinformatics Stack Exchange! 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. Retrying with flexible solve.Solving environment: Found conflicts! trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : now when I tried installing the missing packages they did install. Installation instructions to use this You signed in with another tab or window. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. R version 3.6.1 (2019-07-05) Thanks for contributing an answer to Stack Overflow! It only takes a minute to sign up. to your account. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: "After the incident", I started to be more careful not to trip over things. 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. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 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: library (olsrr) - Error - General - RStudio Community To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Traffic: 307 users visited in the last hour, I am new to all this! [16] phyloseq1.30.0, loaded via a namespace (and not attached): I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked As such there are two solutions that may be more or less attainable given your own IT system. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Please try reinstalling rlang on a fresh session. I tried again and again was met with missing packages BUT!!! Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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 Solution To resolve this error, install the required package as a cluster-installed library. nnet, spatial, survival. More info about Internet Explorer and Microsoft Edge. ()library(DESeq2):Error in loadNamespace: no package called ""s Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub 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. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Acidity of alcohols and basicity of amines. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. DESeq2: Error: package or namespace load failed for 'DESeq2': objects Join us at CRISPR workshops in Koper, Slovenia in 2023. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Content type 'application/zip' length 386703 bytes (377 KB) 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 If you preorder a special airline meal (e.g. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? + "htmlTable", "xfun" From the console install.packages ("rlang") should fix this. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I can download DESeq2 using, User Agreement and Privacy Language(R, Python, SQL) Have a question about this project? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib I thought that working in a new environment would help, but it didnt. package in your R session. 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. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Fortunately I was able to solve it by doing things from several suggested solutions. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Warning: restored xfun, The downloaded binary packages are in 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 If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Are you sure the R you're running from the command line is installed through Anaconda as well? No error messages are returned. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. :), BiocManager::install("locift") and then updating the packages that command indicates. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): The best answers are voted up and rise to the top, Not the answer you're looking for? Hello, 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'. Try installing zip, and then loading olsrr. R DESeq2 - + ), update = TRUE, ask = FALSE) Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide.