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. I tried again and again was met with missing packages BUT!!! In install.packages() : [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4
()library(DESeq2):Error in loadNamespace: no package called ""s Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Are you sure the R you're running from the command line is installed through Anaconda as well? 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. But I guess you have many problems with your installation, and I'd suggest. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages library(caret) namespace load failed Object sigma not found caret , . So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. and then updating the packages that command indicates. 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. The best answers are voted up and rise to the top, Not the answer you're looking for? 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'. 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: Installing Hmisc as suggested above did not solve the issue. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7
Well occasionally send you account related emails. May I know is there any other approach I can try? Is there anyone the same as mine error while loading library(DESeq2)? installation of package GenomeInfoDbData had non-zero exit status. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy.
Error: package or namespace load failed, object not found [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. I tried to download the "locfit" package but I can't find it anywhere. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Running.
Why is this sentence from The Great Gatsby grammatical? May be the version has problem How can I do ? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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"). 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). Policy. Find centralized, trusted content and collaborate around the technologies you use most. R version 3.6.3 (2020-02-29) trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' How do you ensure that a red herring doesn't violate Chekhov's gun? 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? Choose Yes. Is there a proper earth ground point in this switch box? [a/s/n]: Styling contours by colour and by line thickness in QGIS. A place where magic is studied and practiced? 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. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Just realize that I need to write the script "library("DESeq2")" before I proceed. To learn more, see our tips on writing great answers. Please try the following steps: Quit all R/Rstudio sessions. By clicking Sign up for GitHub, you agree to our terms of service and I thought that working in a new environment would help, but it didnt. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Warning: restored xfun, The downloaded binary packages are in Let me confer with the team. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Just to add on -- do you require an old version of Bioconductor for your current project? Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Thanks for contributing an answer to Bioinformatics Stack Exchange! [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: 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 . CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. 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. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. To view documentation for the version of this package installed
Error when installing Aldex2 - Community Plugin Support - Open Source Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat 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"). 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]]) : 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. install.packages('
', repo='http://nbcgib.uesc.br/mirrors/cran/'). nnet, spatial, survival. if (!require("BiocManager", quietly = TRUE)) This includes any installed libraries. Finally After 3-4 manual installations of missing packages everything worked. :), BiocManager::install("locift") I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Platform: x86_64-apple-darwin13.4.0 (64-bit) 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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? You signed in with another tab or window. March 1, 2023, 8:52pm Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. DESeq2 - I can't get the library to load - Bioconductor I am also encountering a set of similar (although possible totally unrelated) issue with other packages, RStudio provides the following warning every startup, library(devtools) gives the following errors, Someone on twitter asked for the results of packageDescription("rlang"). Making statements based on opinion; back them up with references or personal experience. Documentation Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Rload failed - Running under: macOS Sierra 10.12.3, locale: [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Also note, however, that the error you got has been associated in the past with mirror outages. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Learn more about Stack Overflow the company, and our products. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open Solution To resolve this error, install the required package as a cluster-installed library. From the console install.packages ("rlang") should fix this. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). R DESeq2 - Installing package(s) 'XML' Find centralized, trusted content and collaborate around the technologies you use most. That plugin is has not been updated to work with later releases of QIIME 2. Should I update the Bioconductor to latest version instead? Retrying with flexible solve.Solving environment: Found conflicts! Looking for incompatible packages. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. You are doing something very wrong when installing your packages. install.packages ("zip") 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. Replacing broken pins/legs on a DIP IC package. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Follow Up: struct sockaddr storage initialization by network format-string. I've copied the output below in case it helps with troubleshooting. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Sign in Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Is a PhD visitor considered as a visiting scholar? I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Try installing zip, and then loading olsrr. Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. March 1, 2023, 4:56pm What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence?