error: package or namespace load failed for 'deseq2
in your system, start R and enter: Follow - the incident has nothing to do with me; can I use this this way? While a notebook is attached to a cluster, the R namespace cannot be refreshed. I also tried something I found on google: but the installation had errors too, I can write them here if needed. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): now when I tried installing the missing packages they did install. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' To subscribe to this RSS feed, copy and paste this URL into your RSS reader. To learn more, see our tips on writing great answers. The package has place the R version constraint. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Platform: x86_64-w64-mingw32/x64 (64-bit) I'm having a similar error, but different package: library("DESeq2") Also make sure that you have RTools.exe installed and working. [69] tidyselect_1.0.0. Sounds like you might have an issue with which R Rstudio is running. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Citation (from within R, To learn more, see our tips on writing great answers. installation of package GenomeInfoDbData had non-zero exit status. In file.copy(savedcopy, lib, recursive = TRUE) : I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Making statements based on opinion; back them up with references or personal experience. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Installing package(s) 'XML' Documentation Sounds like there might be an issue with conda setup? Thanks for contributing an answer to Stack Overflow! Choose Yes. 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. ERROR: lazy loading failed for package Hmisc Surly Straggler vs. other types of steel frames. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': March 1, 2023, 8:52pm locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 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. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Policy. vegan) just to try it, does this inconvenience the caterers and staff? [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Solving environment: Found conflicts! I would recommend installing an older version of QIIME 2 for this plugin to work. Is there anyone the same as mine error while loading library(DESeq2)? 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: [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 This topic was automatically closed 21 days after the last reply. One solution is to find all available packages. Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 so I would try to use BiocManager::install("XML"). Content type 'application/zip' length 4255589 bytes (4.1 MB) If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Post questions about Bioconductor install.packages ("zip") How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Just updated my previous R to 4.01 and now I cant load DESeq2. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? 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. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Finally After 3-4 manual installations of missing packages everything worked. Feedback RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE 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"). [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Running under: macOS Catalina 10.15.3, Matrix products: default 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. R version 3.6.1 (2019-07-05) 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. Erasmus+ funds available! Have a question about this project? Asking for help, clarification, or responding to other answers. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Hello, And finally, install the problem packages, perhaps also DESeq2. Running. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Try again and choose No. Asking for help, clarification, or responding to other answers. Warning message: package rlang was built under R version 3.5.1. data . check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. You are doing something very wrong when installing your packages. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Running under: macOS Sierra 10.12.6. call: dots_list() 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. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat "4.2") and enter: For older versions of R, please refer to the appropriate Should I update the Bioconductor to latest version instead? Are you sure the R you're running from the command line is installed through Anaconda as well? Then I reinstalled R then Rstudio then RTools. I even tried BiocManager::install("XML") but all failed as shown below. Policy. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Language(R, Python, SQL) The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . If you have a query related to it or one of the replies, start a new topic and refer back with a link. Already on GitHub? 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. Is there a proper earth ground point in this switch box? Use of this site constitutes acceptance of our User Agreement and Privacy [13] ggplot23.3.0 car3.0-7 carData3.0-3 This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Not the answer you're looking for? Open Source Biology & Genetics Interest Group. Is there a single-word adjective for "having exceptionally strong moral principles"? [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in March 1, 2023, 3:25pm Let me confer with the team. Why do many companies reject expired SSL certificates as bugs in bug bounties? a, There are binary versions available but the source versions are later: New replies are no longer allowed. 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. 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. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [5] IRanges_2.8.1 S4Vectors_0.12.1 Press CTRL-C to abort. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. What is the output of. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib I just figured Id ask. How to use Slater Type Orbitals as a basis functions in matrix method correctly? Traffic: 307 users visited in the last hour, I am new to all this! [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: to your account. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Policy. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? there is no package called data.table To view documentation for the version of this package installed . To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Is a PhD visitor considered as a visiting scholar? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 To learn more, see our tips on writing great answers. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Thanks for contributing an answer to Stack Overflow! [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Bioconductor release. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). Content type 'application/zip' length 386703 bytes (377 KB) If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. March 1, 2023, 4:56pm So, supposedly the issue is with Hmisc. Just realize that I need to write the script "library("DESeq2")" before I proceed. No error messages are returned. Styling contours by colour and by line thickness in QGIS. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Installing Hmisc as suggested above did not solve the issue. Any suggestions would be greatly appreciated. (Factorization). Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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"). 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. After 3-4 manual installs everything worked. How do you ensure that a red herring doesn't violate Chekhov's gun? You signed in with another tab or window. failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: q2-aldex2 -> python=3.6 Your python: python=3.8.15 [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): - the incident has nothing to do with me; can I use this this way? Warning message: Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Why is this sentence from The Great Gatsby grammatical? Loading required package: GenomicRanges Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. What am I doing wrong here in the PlotLegends specification? 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. + ), update = TRUE, ask = FALSE) Making statements based on opinion; back them up with references or personal experience. I tried again and again was met with missing packages BUT!!! install.packages('
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