'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Does anyone know why I'm getting the following message when I load tidyverse in a new session. The error states that the current version is 0.4.5 but 0.4.10 is required. But I guess you have many problems with your installation, and I'd suggest. How to use Slater Type Orbitals as a basis functions in matrix method correctly? Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' What do I need to do to reproduce your problem? Fortunately I was able to solve it by doing things from several suggested solutions. package rlang was built under R version 3.5.1. 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. R version 3.6.3 (2020-02-29) DESeq2 installation in R - Bioconductor 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. What is the output of. A place where magic is studied and practiced? I highly recommend that any R/RStudio version not installed inside conda be removed. Policy. install.packages ("zip") Solution To resolve this error, install the required package as a cluster-installed library. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? 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. install.packages("BiocManager"), I get this error: The other option is to download and older version of locfit from the package archive and install manually. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) data . Policy. Installing package(s) 'GenomeInfoDbData' library(DESeq2) Warning: restored xfun, The downloaded binary packages are in there is no package called Hmisc. @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. in your system, start R and enter: Follow How can we prove that the supernatural or paranormal doesn't exist? [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Connect and share knowledge within a single location that is structured and easy to search. Try again and choose No. Looking for incompatible packages.This can take several minutes. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. How do you ensure that a red herring doesn't violate Chekhov's gun? Warning message: [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Sounds like you might have an issue with which R Rstudio is running. 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. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib After 3-4 manual installs everything worked. vegan) just to try it, does this inconvenience the caterers and staff? Whats the grammar of "For those whose stories they are"? Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? 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. I hope you can see something I can't see and help me solving this issue. This can take several minutes. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. "After the incident", I started to be more careful not to trip over things. enter citation("DESeq2")): To install this package, start R (version However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Post questions about Bioconductor Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Use of this site constitutes acceptance of our User Agreement and Privacy Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Hello, 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. [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. Platform: x86_64-apple-darwin17.0 (64-bit) [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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: To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. You signed in with another tab or window. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 I thought that working in a new environment would help, but it didnt. 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. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Making statements based on opinion; back them up with references or personal experience. Asking for help, clarification, or responding to other answers. "4.2") and enter: For older versions of R, please refer to the appropriate [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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 . Any suggestions would be greatly appreciated. Retrying with flexible solve.Solving environment: Found conflicts! Did you do that? 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]]): [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Running under: macOS Catalina 10.15.3, Matrix products: default rev2023.3.3.43278. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib We've tried this - and can replicate this issue on a completely new install with no existing package installs. Error when installing Aldex2 - Community Plugin Support - Open Source Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. How can I fix error with loading package in R ? | ResearchGate /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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. [1] stats4 parallel stats graphics grDevices utils Not the answer you're looking for? I have tried your suggestion and also updating the packages that command indicates. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 I am running a new install of R (3.5.0) and RStudio (1.1.414). Please remember to confirm an answer once you've received one. Why do many companies reject expired SSL certificates as bugs in bug bounties? Language(R, Python, SQL) 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. Surly Straggler vs. other types of steel frames. I guess that means we can finally close this issue. Find centralized, trusted content and collaborate around the technologies you use most. How to notate a grace note at the start of a bar with lilypond? I tried following the instructions for 2019.7 as well and I am getting the same error. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: When an R package depends on a newer package version, the required package is downloaded but not loaded. Platform: x86_64-apple-darwin13.4.0 (64-bit) Install DESeq2 through anaconda - Bioinformatics Stack Exchange [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 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: Running. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Press CTRL-C to abort. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). rev2023.3.3.43278. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Policy. To learn more, see our tips on writing great answers. 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. Is a PhD visitor considered as a visiting scholar? Old packages: 'RcppArmadillo', 'survival' package xfun successfully unpacked and MD5 sums checked Platform: x86_64-apple-darwin15.6.0 (64-bit) 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 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Looking for incompatible packages. Is there anyone the same as mine error while loading library(DESeq2)? It only takes a minute to sign up. Installing package(s) 'XML' Error: package or namespace load failed for 'DESeq2 - Bioconductor Connect and share knowledge within a single location that is structured and easy to search. 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 and then updating the packages that command indicates. Running under: macOS Sierra 10.12.6. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. March 1, 2023, 7:31pm 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. 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. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( C:\R\R-3.4.3\library). Update all/some/none? [13] ggplot23.3.0 car3.0-7 carData3.0-3 Loading required package: GenomicRanges 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. To resolve this error, install the required package as a cluster-installed library. I need help installing a package "DESeq2" having - RStudio Community Making statements based on opinion; back them up with references or personal experience. 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. The best answers are voted up and rise to the top, Not the answer you're looking for? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Sounds like there might be an issue with conda setup? Convince your IT department to relax the permissions for R 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. 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). When you load the package, you can observe this error. Then I reinstalled R then Rstudio then RTools. In file.copy(savedcopy, lib, recursive = TRUE) : installation of package GenomeInfoDbData had non-zero exit status. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Documentation 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). 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. In addition: Warning message: nnet, spatial, survival I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. install.packages('
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