error: package or namespace load failed for 'deseq2

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. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Have you tried install.packages("locfit") ? Give up and run everything from the "permitted" library location (e.g. March 1, 2023, 8:52pm 4. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Is the God of a monotheism necessarily omnipotent? [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. R version 4.0.1 (2020-06-06) March 1, 2023, 7:31pm Policy. 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). How can we prove that the supernatural or paranormal doesn't exist? Find centralized, trusted content and collaborate around the technologies you use most. rev2023.3.3.43278. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 "4.2") and enter: For older versions of R, please refer to the appropriate 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. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Why are physically impossible and logically impossible concepts considered separate in terms of probability? [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 This topic was automatically closed 21 days after the last reply. it would be good to hear any speculation you have of how this might have happened). 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 . Should I update the Bioconductor to latest version instead? To learn more, see our tips on writing great answers. I hope you can see something I can't see and help me solving this issue. When you load the package, you can observe this error. 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. library(caret) namespace load failed Object sigma not found caret , . - the incident has nothing to do with me; can I use this this way? Running under: macOS Sierra 10.12.6. 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. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? there is no package called Hmisc. Then I reinstalled R then Rstudio then RTools. C:\R\R-3.4.3\library). Try again and choose No. 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 think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Sounds like you might have an issue with which R Rstudio is running. (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 . [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 I'm having a similar error, but different package: library("DESeq2") [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. 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. 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'. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, now when I tried installing the missing packages they did install. Warning: restored xfun, The downloaded binary packages are in sessionInfo() Solution To resolve this error, install the required package as a cluster-installed library. "After the incident", I started to be more careful not to trip over things. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 I then launched the R application (from the finder, not RStudio) and installed BiocManager. Surly Straggler vs. other types of steel frames. Installing package(s) 'GenomeInfoDbData' RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) package xfun successfully unpacked and MD5 sums checked running multiple versions of the same package, keeping separate libraries for some projects). Any other suggestion? [7] datasets methods base, other attached packages: [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 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). How do I align things in the following tabular environment? @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. 9. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 there is no package called data.table How do you ensure that a red herring doesn't violate Chekhov's gun? Please remember to confirm an answer once you've received one. Use of this site constitutes acceptance of our User Agreement and Privacy If it fails, required operating system facilities are missing. Statistics ; Algorithm(ML, DL,.) ERROR: dependency Hmisc is not available for package DESeq2 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). biocLite(), install.packages() (and the devtools equivalent?) in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Whats the grammar of "For those whose stories they are"? 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. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. [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: installation of package GenomeInfoDbData had non-zero exit status. I tried to download the "locfit" package but I can't find it anywhere. Traffic: 307 users visited in the last hour, I am new to all this! I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Policy. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Sign in Not the answer you're looking for? Well occasionally send you account related emails. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Did you do that? Old packages: 'RcppArmadillo', 'survival' [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 A place where magic is studied and practiced? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Policy. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. nnet, spatial, survival How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? 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. Learn more about Stack Overflow the company, and our products. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. Policy. install.packages ("zip") ERROR: lazy loading failed for package Hmisc If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Thanks for contributing an answer to Stack Overflow! 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 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Warning message: Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Remember to always click on the red Show me the content on this page notice when navigating these older versions. You signed in with another tab or window. If you have a query related to it or one of the replies, start a new topic and refer back with a link. Making statements based on opinion; back them up with references or personal experience. To add to this, I have also been using DESeq2 recently and ran into the same problem. What is a word for the arcane equivalent of a monastery? install.packages("BiocManager"), I get this error: By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Content type 'application/zip' length 4255589 bytes (4.1 MB) guide. error: object 'rlang_dots_list' not found [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Is there a proper earth ground point in this switch box? Retrying with flexible solve.Solving environment: Found conflicts! The package has place the R version constraint. Whats the grammar of "For those whose stories they are"? install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Already on GitHub? package rlang was built under R version 3.5.1. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 I guess that means we can finally close this issue. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. I am running a new install of R (3.5.0) and RStudio (1.1.414). Use MathJax to format equations. nnet, spatial, survival. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. I was assuming that to be the case. sessionInfo() Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): MathJax reference. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Connect and share knowledge within a single location that is structured and easy to search. Are there tables of wastage rates for different fruit and veg? "After the incident", I started to be more careful not to trip over things. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. 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"). To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Please try the following steps: Quit all R/Rstudio sessions. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. + "htmlTable", "xfun" Use of this site constitutes acceptance of our User Agreement and Privacy Find centralized, trusted content and collaborate around the technologies you use most. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Installing Hmisc as suggested above did not solve the issue. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Running under: Windows 10 x64 (build 18362), locale: Fortunately I was able to solve it by doing things from several suggested solutions. 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. While a notebook is attached to a cluster, the R namespace cannot be refreshed. By clicking Sign up for GitHub, you agree to our terms of service and What am I doing wrong here in the PlotLegends specification? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Bad: conda install -c bioconda bioconductor-deseq2. 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. This article explains how to resolve the package or namespace loading error. [7] edgeR_3.16.5 limma_3.30.12 I installed the package successfully with conda, but Rstudio is apparently does not know about it. I would recommend installing an older version of QIIME 2 for this plugin to work. 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. After 3-4 manual installs everything worked. Installing package(s) 'htmlTable', 'xfun' Why is this sentence from The Great Gatsby grammatical? 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. .onLoad failed in loadNamespace() for 'rlang', details: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Acidity of alcohols and basicity of amines. 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 You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. 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 ("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. 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 . In install.packages() : Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. @artembus Sounds like it was a ton of work! 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"). 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. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Convince your IT department to relax the permissions for R packages * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc What is the output of. 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. binary source needs_compilation 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). Platform: x86_64-apple-darwin15.6.0 (64-bit) [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Glad everything is finally working now. Post questions about Bioconductor Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. privacy statement. 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. It is working now. call: dots_list() [69] tidyselect_1.0.0. Installation instructions to use this What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Feedback We've tried this - and can replicate this issue on a completely new install with no existing package installs. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 So, supposedly the issue is with Hmisc. Choose Yes. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Use of this site constitutes acceptance of our User Agreement and Privacy Installing package(s) 'XML' The best answers are voted up and rise to the top, Not the answer you're looking for? But I guess you have many problems with your installation, and I'd suggest. Asking for help, clarification, or responding to other answers. 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: Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Is there a single-word adjective for "having exceptionally strong moral principles"? May be the version has problem How can I do ? Just updated my previous R to 4.01 and now I cant load DESeq2. 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. + ), update = TRUE, ask = FALSE) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Is there anything I can do to speed it up? (Factorization). Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. How to use Slater Type Orbitals as a basis functions in matrix method correctly? [1] stats4 parallel stats graphics grDevices utils 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. 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. I have tried your suggestion and also updating the packages that command indicates. R version 3.6.1 (2019-07-05) Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Try installing zip, and then loading olsrr. there is no package called GenomeInfoDbData The other option is to download and older version of locfit from the package archive and install manually. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Any suggestions would be greatly appreciated. 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? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. May I know is there any other approach I can try? @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. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 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. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. How to use Slater Type Orbitals as a basis functions in matrix method correctly? Press CTRL-C to abort. data . trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' And finally, install the problem packages, perhaps also DESeq2. Solving environment: Found conflicts! I'm trying to reproduce your problem, so being as precise as possible is important. a, There are binary versions available but the source versions are later: I do know that it works well in qiime2-2020.6. 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 Running. I would like to install DESeq2 for DE analysis. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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 In file.copy(savedcopy, lib, recursive = TRUE) : Why do academics stay as adjuncts for years rather than move around? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Join us at CRISPR workshops in Koper, Slovenia in 2023. Update all/some/none? enter citation("DESeq2")): To install this package, start R (version :), BiocManager::install("locift") Policy. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Content type 'application/zip' length 233860 bytes (228 KB) Platform: x86_64-apple-darwin17.0 (64-bit) Erasmus+ funds available! More info about Internet Explorer and Microsoft Edge. there is no package called Hmisc. Connect and share knowledge within a single location that is structured and easy to search. Thanks! Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Hello, if (!require("BiocManager", quietly = TRUE)) The error states that the current version is 0.4.5 but 0.4.10 is required. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 If you preorder a special airline meal (e.g.
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