error: package or namespace load failed for 'deseq2
Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). 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. It only takes a minute to sign up. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Sounds like you might have an issue with which R Rstudio is running. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [7] datasets methods base, other attached packages: 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. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. So if you still get this error try changing your CRAN mirror. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: I would recommend installing an older version of QIIME 2 for this plugin to work. Thanks for contributing an answer to Stack Overflow! Running under: Windows 10 x64 (build 18362), locale: Surly Straggler vs. other types of steel frames. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. 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) Surly Straggler vs. other types of steel frames. 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. Replacing broken pins/legs on a DIP IC package. R version 4.0.1 (2020-06-06) [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Do I need a thermal expansion tank if I already have a pressure tank? Running under: macOS Sierra 10.12.3, locale: [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Give up and run everything from the "permitted" library location (e.g. Is a PhD visitor considered as a visiting scholar? rev2023.3.3.43278. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 R| - 9. Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Installing package(s) 'XML' Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) @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. This article explains how to resolve the package or namespace loading error. Language(R, Python, SQL) Is the God of a monotheism necessarily omnipotent? Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. I tried again and again was met with missing packages BUT!!! As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [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: I can download DESeq2 using, User Agreement and Privacy check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Loading required package: GenomeInfoDb I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. I need help installing a package "DESeq2" having - RStudio Community locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 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. What is the output of. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Warning: cannot remove prior installation of package xfun The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. ERROR: lazy loading failed for package Hmisc The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Making statements based on opinion; back them up with references or personal experience. Also note, however, that the error you got has been associated in the past with mirror outages. I would like to install DESeq2 for DE analysis. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Also make sure that you have RTools.exe installed and working. and then updating the packages that command indicates. Are you sure the R you're running from the command line is installed through Anaconda as well? library(DESeq2) [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Retrying with flexible solve.Solving environment: Found conflicts! I then launched the R application (from the finder, not RStudio) and installed BiocManager. I just figured Id ask. 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 Warning message: I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. One solution is to find all available packages. Are there tables of wastage rates for different fruit and veg? Platform: x86_64-apple-darwin17.0 (64-bit) Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages - the incident has nothing to do with me; can I use this this way? there is no package called data.table rev2023.3.3.43278. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: More info about Internet Explorer and Microsoft Edge. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). call: dots_list() there is no package called GenomeInfoDbData What do I need to do to reproduce your problem? [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 R version 3.6.3 (2020-02-29) I was assuming that to be the case. What am I doing wrong here in the PlotLegends specification? /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Sorry, I'm newbie. In install.packages() : That plugin is has not been updated to work with later releases of QIIME 2. so I would try to use BiocManager::install("XML"). A place where magic is studied and practiced? Any other suggestion? Is it suspicious or odd to stand by the gate of a GA airport watching the planes? I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Running. Then I reinstalled R then Rstudio then RTools. We've tried this - and can replicate this issue on a completely new install with no existing package installs. error: object 'rlang_dots_list' not found Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 I tried to download the "locfit" package but I can't find it anywhere. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. May be the version has problem How can I do ? install.packages('
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