library(DESeq2) What do I need to do to reproduce your problem? library(caret) namespace load failed Object sigma not Asking for help, clarification, or responding to other answers. biocLite(), install.packages() (and the devtools equivalent?) Also note, however, that the error you got has been associated in the past with mirror outages. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib When you load the package, you can observe this error. I hope you can see something I can't see and help me solving this issue. [40] assertthat_0.1 rpart_4.1-10 nnet_7.3-12, It should not be necessary (R should take care of loading dependencies) but try installating data.table also. Policy. Loading required package: GenomicRanges Choose Yes. 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. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 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. package in your R session. 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. Running. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 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). [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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. This article explains how to resolve the package or namespace loading error. Content type 'application/zip' length 386703 bytes (377 KB) Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Is there anything I can do to speed it up? I'm trying to reproduce your problem, so being as precise as possible is important. Sounds like there might be an issue with conda setup? [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Start R to confirm they are gone. I am running a new install of R (3.5.0) and RStudio (1.1.414). to allow custom library locations. 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. Use this. More info about Internet Explorer and Microsoft Edge. Please remember to confirm an answer once you've received one. "4.2") and enter: For older versions of R, please refer to the appropriate Is there a proper earth ground point in this switch box? I need help installing a package "DESeq2" having - RStudio Community 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. Documentation But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Running under: Windows 10 x64 (build 18362), locale: [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Traffic: 307 users visited in the last hour, I am new to all this! dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext May be the version has problem How can I do ? Connect and share knowledge within a single location that is structured and easy to search. error: object 'rlang_dots_list' not found [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Well occasionally send you account related emails. there is no package called GenomeInfoDbData Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 9. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. March 1, 2023, 7:31pm 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 [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Thanks! Is there a proper earth ground point in this switch box? It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Why do many companies reject expired SSL certificates as bugs in bug bounties? Thanks for contributing an answer to Stack Overflow! Follow Up: struct sockaddr storage initialization by network format-string. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Why is there a voltage on my HDMI and coaxial cables? if (!require("BiocManager", quietly = TRUE)) New replies are no longer allowed. install.packages("BiocManager"), I get this error: rev2023.3.3.43278. Warning: restored xfun, The downloaded binary packages are in Platform: x86_64-apple-darwin17.0 (64-bit) /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages so I would try to use BiocManager::install("XML"). [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: + ), update = TRUE, ask = FALSE) 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'. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 vegan) just to try it, does this inconvenience the caterers and staff? 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). [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 @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. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 If you try loading the DEseq2 library now, that might work. 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]]) : Use of this site constitutes acceptance of our User Agreement and Privacy Post questions about Bioconductor running multiple versions of the same package, keeping separate libraries for some projects). RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : 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 Content type 'application/zip' length 233860 bytes (228 KB) Does a summoned creature play immediately after being summoned by a ready action? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? After 3-4 manual installs everything worked. Just updated my previous R to 4.01 and now I cant load DESeq2. Policy. Thanks for contributing an answer to Stack Overflow! Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Content type 'application/zip' length 4255589 bytes (4.1 MB) [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 :), BiocManager::install("locift") Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Use MathJax to format equations. I can download DESeq2 using, User Agreement and Privacy 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 'XML' so I would try to use BiocManager::install ("XML"). I tried to download the "locfit" package but I can't find it anywhere. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. 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. + "htmlTable", "xfun" there is no package called locfit. Making statements based on opinion; back them up with references or personal experience. nnet, spatial, survival. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [16] phyloseq1.30.0, loaded via a namespace (and not attached): [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 I do know that it works well in qiime2-2020.6. privacy statement. 2. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 What is the output of. Not the answer you're looking for? Policy. If you have a query related to it or one of the replies, start a new topic and refer back with a link. Connect and share knowledge within a single location that is structured and easy to search. 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: Looking for incompatible packages. Bioconductor release. .onLoad failed in loadNamespace() for 'rlang', details: The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. "After the incident", I started to be more careful not to trip over things. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Already on GitHub? 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. The package has place the R version constraint. 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. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? rev2023.3.3.43278. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages You signed in with another tab or window. 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. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 rstudio - Error: package or namespace load failed for 'tidyverse [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Erasmus+ funds available! downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Have a question about this project? [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 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. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. 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. - the incident has nothing to do with me; can I use this this way? [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Does anyone know why I'm getting the following message when I load tidyverse in a new session. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 data . Platform: x86_64-apple-darwin15.6.0 (64-bit) nnet, spatial, survival To view documentation for the version of this package installed downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. Also make sure that you have RTools.exe installed and working. Give up and run everything from the "permitted" library location (e.g. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. DESeq2_2301_76497647-CSDN I've copied the output below in case it helps with troubleshooting. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Then I reinstalled R then Rstudio then RTools. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Update all/some/none? 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. If you preorder a special airline meal (e.g. The best answers are voted up and rise to the top, Not the answer you're looking for? How do I align things in the following tabular environment? Replacing broken pins/legs on a DIP IC package. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Find centralized, trusted content and collaborate around the technologies you use most. there is no package called Hmisc. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. DESeq2 installation in R - Bioconductor By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 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. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 "After the incident", I started to be more careful not to trip over things. Whats the grammar of "For those whose stories they are"? 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: How to use Slater Type Orbitals as a basis functions in matrix method correctly? Thanks for contributing an answer to Bioinformatics Stack Exchange! Installing package(s) 'htmlTable', 'xfun' Warning message: Policy. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? I'm having a similar error, but different package: library("DESeq2") Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. a, There are binary versions available but the source versions are later: 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. Not the answer you're looking for? Retrying with flexible solve.Solving environment: Found conflicts! To learn more, see our tips on writing great answers. Are you sure the R you're running from the command line is installed through Anaconda as well? Please read the posting Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Running under: macOS Sierra 10.12.6. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Is there a single-word adjective for "having exceptionally strong moral principles"? [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: now when I tried installing the missing packages they did install. How to notate a grace note at the start of a bar with lilypond? Learn more about Stack Overflow the company, and our products. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Why is this sentence from The Great Gatsby grammatical? Making statements based on opinion; back them up with references or personal experience. Use of this site constitutes acceptance of our User Agreement and Privacy trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' library (olsrr) - Error - General - RStudio Community Then I reinstalled R then Rstudio then RTools. there is no package called GenomeInfoDbData Solution To resolve this error, install the required package as a cluster-installed library. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 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. 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 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. Find centralized, trusted content and collaborate around the technologies you use most. it would be good to hear any speculation you have of how this might have happened). Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): rev2023.3.3.43278. I also tried something I found on google: but the installation had errors too, I can write them here if needed. Language(R, Python, SQL) Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' - the incident has nothing to do with me; can I use this this way? Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. R| - Press CTRL-C to abort. there is no package called Hmisc. When an R package depends on a newer package version, the required package is downloaded but not loaded. I would recommend installing an older version of QIIME 2 for this plugin to work. Acidity of alcohols and basicity of amines. Installing Hmisc as suggested above did not solve the issue. 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. Why do academics stay as adjuncts for years rather than move around? call: dots_list() We've tried this - and can replicate this issue on a completely new install with no existing package installs. Styling contours by colour and by line thickness in QGIS. In install.packages() : You are doing something very wrong when installing your packages. 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 have tried your suggestion and also updating the packages that command indicates. This includes any installed libraries. ()library(DESeq2):Error in loadNamespace: no package called ""s Platform: x86_64-w64-mingw32/x64 (64-bit) What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Why do academics stay as adjuncts for years rather than move around? /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Surly Straggler vs. other types of steel frames. To add to this, I have also been using DESeq2 recently and ran into the same problem. 4. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in 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. Installing package(s) 'XML' To subscribe to this RSS feed, copy and paste this URL into your RSS reader. How can I fix error with loading package in R ? | ResearchGate C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Policy. binary source needs_compilation I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Statistics ; Algorithm(ML, DL,.) In file.copy(savedcopy, lib, recursive = TRUE) : 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. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open Why are physically impossible and logically impossible concepts considered separate in terms of probability? . I highly recommend that any R/RStudio version not installed inside conda be removed. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Sign in 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"). MathJax reference. Warning message: Join us at CRISPR workshops in Koper, Slovenia in 2023. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Remember to always click on the red Show me the content on this page notice when navigating these older versions. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [R] Error: package or namespace load failed for 'ggplot2' in So, supposedly the issue is with Hmisc. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. R version 3.6.3 (2020-02-29) [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): What am I doing wrong here in the PlotLegends specification? Open Source Biology & Genetics Interest Group. 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. C:\R\R-3.4.3\library). You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Have you tried install.packages("locfit") ? It is working now. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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). A place where magic is studied and practiced? What is a word for the arcane equivalent of a monastery? Whats the grammar of "For those whose stories they are"? This can take several minutes. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. How can we prove that the supernatural or paranormal doesn't exist? Running under: macOS Catalina 10.15.3, Matrix products: default I then launched the R application (from the finder, not RStudio) and installed BiocManager. Sounds like you might have an issue with which R Rstudio is running. 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'. DESeq2: Error: package or namespace load failed for 'DESeq2': objects How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Solving environment: Found conflicts! Citation (from within R, @artembus Sounds like it was a ton of work! 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.