error: package or namespace load failed for 'deseq2glenn taylor obituary
Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. By clicking Sign up for GitHub, you agree to our terms of service and (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 . - the incident has nothing to do with me; can I use this this way? I've previously written a blog post about this topic, and I can say from experience that installing R packages through conda can cause lots of headaches. Traffic: 307 users visited in the last hour, I am new to all this! DESeq2 installation in R - Bioconductor 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. Platform: x86_64-w64-mingw32/x64 (64-bit) 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: Let me confer with the team. If you preorder a special airline meal (e.g. binary source needs_compilation there is no package called Hmisc. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Remember to always click on the red Show me the content on this page notice when navigating these older versions. Error when installing Aldex2 - Community Plugin Support - Open Source 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. if (!require("BiocManager", quietly = TRUE)) 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. MathJax reference. Installing package(s) 'GenomeInfoDbData' there is no package called GenomeInfoDbData March 1, 2023, 7:31pm Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Try again and choose No. 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. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? When an R package depends on a newer package version, the required package is downloaded but not loaded. Please try reinstalling rlang on a fresh session. Does a summoned creature play immediately after being summoned by a ready action? or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. 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. [13] ggplot23.3.0 car3.0-7 carData3.0-3 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. Follow Up: struct sockaddr storage initialization by network format-string. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. After 3-4 manual installs everything worked. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Give up and run everything from the "permitted" library location (e.g. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Policy. there is no package called Hmisc. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Policy. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib privacy statement. Sorry, I'm newbie. Running under: macOS Sierra 10.12.3, locale: The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 The best answers are voted up and rise to the top, Not the answer you're looking for? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Content type 'application/zip' length 4255589 bytes (4.1 MB) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). March 1, 2023, 8:52pm locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) and then updating the packages that command indicates. there is no package called data.table Sounds like there might be an issue with conda setup? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Please remember to confirm an answer once you've received one. Feedback Start R to confirm they are gone. 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. 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'. Why do many companies reject expired SSL certificates as bugs in bug bounties? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Looking for incompatible packages. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Also make sure that you have RTools.exe installed and working. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Are there tables of wastage rates for different fruit and veg? a, There are binary versions available but the source versions are later: [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 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. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [69] tidyselect_1.0.0. so I would try to use BiocManager::install("XML"). A place where magic is studied and practiced? Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in 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. 1. install.packages("BiocManager"), I get this error: [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Replacing broken pins/legs on a DIP IC package. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Warning message: library(caret) namespace load failed Object sigma not Sounds like you might have an issue with which R Rstudio is running. @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. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 How to notate a grace note at the start of a bar with lilypond? To add to this, I have also been using DESeq2 recently and ran into the same problem. Already on GitHub? How do I align things in the following tabular environment? Is a PhD visitor considered as a visiting scholar? Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Retrying with flexible solve.Solving environment: Found conflicts! I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. package xfun successfully unpacked and MD5 sums checked That plugin is has not been updated to work with later releases of QIIME 2. 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). Learn more about Stack Overflow the company, and our products. Whats the grammar of "For those whose stories they are"? Try installing zip, and then loading olsrr. Policy. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open 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. Convince your IT department to relax the permissions for R packages [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 If not fixed, Try removing remove.packages (rlang) then. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 in your system, start R and enter: Follow You are doing something very wrong when installing your packages. [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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). So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Just to add on -- do you require an old version of Bioconductor for your current project? "After the incident", I started to be more careful not to trip over things. Running under: macOS Catalina 10.15.3, Matrix products: default library(caret) namespace load failed Object sigma not found caret , . [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 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 Use of this site constitutes acceptance of our User Agreement and Privacy Is there a single-word adjective for "having exceptionally strong moral principles"? Error: package or namespace load failed, object not found Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. This topic was automatically closed 21 days after the last reply. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Resolving package or namespace loading error The other option is to download and older version of locfit from the package archive and install manually. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Should I update the Bioconductor to latest version instead? Just updated my previous R to 4.01 and now I cant load DESeq2. Is there anyone the same as mine error while loading library(DESeq2)? I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Join us at CRISPR workshops in Koper, Slovenia in 2023. 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. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. biocLite(), install.packages() (and the devtools equivalent?) 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
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