To learn more, see our tips on writing great answers. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Connect and share knowledge within a single location that is structured and easy to search. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Thanks for contributing an answer to Stack Overflow! Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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. R version 3.6.3 (2020-02-29) Bioconductor release. 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. How do I align things in the following tabular environment? The best answers are voted up and rise to the top, Not the answer you're looking for? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Retrying with flexible solve.Solving environment: Found conflicts! 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in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and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]]): I tried to download the "locfit" package but I can't find it anywhere. 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. Open Source Biology & Genetics Interest Group. Platform: x86_64-w64-mingw32/x64 (64-bit) [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 in your system, start R and enter: Follow to allow custom library locations. Please read the posting As such there are two solutions that may be more or less attainable given your own IT system. Whats the grammar of "For those whose stories they are"? - the incident has nothing to do with me; can I use this this way? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Why is this sentence from The Great Gatsby grammatical? 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. C:\R\R-3.4.3\library). library(DESeq2) Error: package GenomeInfoDb could not be loaded. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 "After the incident", I started to be more careful not to trip over things. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, When an R package depends on a newer package version, the required package is downloaded but not loaded. I have tried your suggestion and also updating the packages that command indicates. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. "After the incident", I started to be more careful not to trip over things. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Surly Straggler vs. other types of steel frames. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Why are physically impossible and logically impossible concepts considered separate in terms of probability? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Fortunately I was able to solve it by doing things from several suggested solutions. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages This includes any installed libraries. a, There are binary versions available but the source versions are later: /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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. Just realize that I need to write the script "library("DESeq2")" before I proceed. 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: requires R 4 and running more than a couple of releases behind in R risks multiplying problems. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Use of this site constitutes acceptance of our User Agreement and Privacy 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. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 This article explains how to resolve the package or namespace loading error. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in enter citation("DESeq2")): To install this package, start R (version Then I reinstalled R then Rstudio then RTools. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). 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 . As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. I installed the package successfully with conda, but Rstudio is apparently does not know about it. data . there is no package called Hmisc. Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. 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. Is there a proper earth ground point in this switch box? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 rev2023.3.3.43278. It only takes a minute to sign up. In file.copy(savedcopy, lib, recursive = TRUE) : How to use Slater Type Orbitals as a basis functions in matrix method correctly? Use of this site constitutes acceptance of our User Agreement and Privacy 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. If not fixed, Try removing remove.packages (rlang) then. there is no package called GenomeInfoDbData 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. Have you tried install.packages("locfit") ? Running under: macOS Sierra 10.12.3, locale: Glad everything is finally working now. privacy statement. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [a/s/n]: Installing package(s) 'GenomeInfoDbData' Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 1. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. so I would try to use BiocManager::install("XML"). That plugin is has not been updated to work with later releases of QIIME 2. I thought that working in a new environment would help, but it didnt. Are there tables of wastage rates for different fruit and veg? I also tried something I found on google: but the installation had errors too, I can write them here if needed. Find centralized, trusted content and collaborate around the technologies you use most. Running under: Windows 10 x64 (build 18362), locale: I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 9. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. sessionInfo() I guess that means we can finally close this issue. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib No error messages are returned. 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). rev2023.3.3.43278. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Also note, however, that the error you got has been associated in the past with mirror outages. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Is there a single-word adjective for "having exceptionally strong moral principles"? Does anyone know why I'm getting the following message when I load tidyverse in a new session. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Follow Up: struct sockaddr storage initialization by network format-string. MathJax reference. Well occasionally send you account related emails. What am I doing wrong here in the PlotLegends specification? Feedback check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. When an R package depends on a newer package version, the required package is downloaded but not loaded. Asking for help, clarification, or responding to other answers. Surly Straggler vs. other types of steel frames. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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.

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