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. I guess that means we can finally close this issue. That plugin is has not been updated to work with later releases of QIIME 2. Does a summoned creature play immediately after being summoned by a ready action? Please try the following steps: Quit all R/Rstudio sessions. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? I'm trying to reproduce your problem, so being as precise as possible is important. I also tried something I found on google: but the installation had errors too, I can write them here if needed. - the incident has nothing to do with me; can I use this this way? Have a question about this project? I would like to install DESeq2 for DE analysis. library(DESeq2) If it fails, required operating system facilities are missing. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 [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: After 3-4 manual installs everything worked. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. March 1, 2023, 8:52pm Should I update the Bioconductor to latest version instead? BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Let me confer with the team. Use this. By clicking Sign up for GitHub, you agree to our terms of service and [a/s/n]: sessionInfo() Convince your IT department to relax the permissions for R packages Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. 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 . Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Erasmus+ funds available! Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Connect and share knowledge within a single location that is structured and easy to search. rev2023.3.3.43278. 1. [7] edgeR_3.16.5 limma_3.30.12 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': 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. .onLoad failed in loadNamespace() for 'rlang', details: [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Connect and share knowledge within a single location that is structured and easy to search. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Running under: macOS Sierra 10.12.6. in your system, start R and enter: Follow 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). /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 [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. package in your R session. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). When an R package depends on a newer package version, the required package is downloaded but not loaded. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Join us at CRISPR workshops in Koper, Slovenia in 2023. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. It only takes a minute to sign up. I highly recommend that any R/RStudio version not installed inside conda be removed. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Making statements based on opinion; back them up with references or personal experience. 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. One solution is to find all available packages. @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. Not the answer you're looking for? A place where magic is studied and practiced? No error messages are returned. library(caret) namespace load failed Object sigma not found caret , . Is there anyone the same as mine error while loading library(DESeq2)? Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? ERROR: dependency Hmisc is not available for package DESeq2 (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 . dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 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. I tried again and again was met with missing packages BUT!!! [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 rev2023.3.3.43278. Any other suggestion? [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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: I tried following the instructions for 2019.7 as well and I am getting the same error. Is there anything I can do to speed it up? I then launched the R application (from the finder, not RStudio) and installed BiocManager. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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? Sounds like you might have an issue with which R Rstudio is running. This includes any installed libraries. 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. How do you ensure that a red herring doesn't violate Chekhov's gun? in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [5] IRanges_2.8.1 S4Vectors_0.12.1 If you try loading the DEseq2 library now, that might work. R version 3.6.3 (2020-02-29) Surly Straggler vs. other types of steel frames. How can we prove that the supernatural or paranormal doesn't exist? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Platform: x86_64-apple-darwin15.6.0 (64-bit) 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. Also note, however, that the error you got has been associated in the past with mirror outages. I've copied the output below in case it helps with troubleshooting. New replies are no longer allowed. Use of this site constitutes acceptance of our User Agreement and Privacy Any suggestions would be greatly appreciated. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Glad everything is finally working now. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. 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"). 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. 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: However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Did you do that? Warning message: Language(R, Python, SQL) Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. I can download DESeq2 using, User Agreement and Privacy Are you sure the R you're running from the command line is installed through Anaconda as well? Solution To resolve this error, install the required package as a cluster-installed library. 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. How to notate a grace note at the start of a bar with lilypond? Please remember to confirm an answer once you've received one. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Error: package GenomeInfoDb could not be loaded. Making statements based on opinion; back them up with references or personal experience. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 The package has place the R version constraint. We've tried this - and can replicate this issue on a completely new install with no existing package installs.