error: package or namespace load failed for 'deseq2is cary stayner still alive

Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? library (olsrr) - Error - General - RStudio Community library(DESeq2) [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Have you tried install.packages("locfit") ? [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Documentation there is no package called Hmisc. But I guess you have many problems with your installation, and I'd suggest. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Open Source Biology & Genetics Interest Group. package xfun successfully unpacked and MD5 sums checked DESeq2_2301_76497647-CSDN 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. DESeq2: Error: package or namespace load failed for 'DESeq2': objects 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. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : privacy statement. Convince your IT department to relax the permissions for R packages downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Bioconductor - DESeq2 [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 installation of package GenomeInfoDbData had non-zero exit status. When you load the package, you can observe this error. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Is the God of a monotheism necessarily omnipotent? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 I'm trying to reproduce your problem, so being as precise as possible is important. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. - the incident has nothing to do with me; can I use this this way? Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Then I reinstalled R then Rstudio then RTools. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' library(caret) namespace load failed Object sigma not found caret , . When an R package depends on a newer package version, the required package is downloaded but not loaded. Please try the following steps: Quit all R/Rstudio sessions. 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 package(s) 'XML' Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat R version 3.6.1 (2019-07-05) A place where magic is studied and practiced? Installing package(s) 'GenomeInfoDbData' Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. 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. [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. In file.copy(savedcopy, lib, recursive = TRUE) : Whats the grammar of "For those whose stories they are"? unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 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. Thank you @hharder. Remember to always click on the red Show me the content on this page notice when navigating these older versions. Platform: x86_64-apple-darwin17.0 (64-bit) Then I reinstalled R then Rstudio then RTools. How to use Slater Type Orbitals as a basis functions in matrix method correctly? error: object 'rlang_dots_list' not found [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: Policy. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 vegan) just to try it, does this inconvenience the caterers and staff? That plugin is has not been updated to work with later releases of QIIME 2. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Well occasionally send you account related emails. How do I align things in the following tabular environment? Install DESeq2 through anaconda - Bioinformatics Stack Exchange Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). I can download DESeq2 using, User Agreement and Privacy 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? ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: 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 May I know is there any other approach I can try? to allow custom library locations. What do I need to do to reproduce your problem? Try again and choose No. 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. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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. March 1, 2023, 4:56pm I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? I've copied the output below in case it helps with troubleshooting. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 install.packages ("zip") Surly Straggler vs. other types of steel frames. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. in your system, start R and enter: Follow [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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. DESeq2 installation in R - Bioconductor 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]]) : Running under: macOS Catalina 10.15.3, Matrix products: default [5] IRanges_2.8.1 S4Vectors_0.12.1 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Please remember to confirm an answer once you've received one. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Replacing broken pins/legs on a DIP IC package. 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. 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. 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. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: 4. 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. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics.

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