While a notebook is attached to a cluster, the R namespace cannot be refreshed. Loading required package: GenomeInfoDb [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 9. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Just realize that I need to write the script "library("DESeq2")" before I proceed. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Installing DESeq2 Error: no package called GenomeInfoDbData, https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz, https://cran.rstudio.com/bin/macosx/contrib/4.0/RcppArmadillo_0.9.880.1.0.tgz, https://cran.rstudio.com/bin/macosx/contrib/4.0/survival_3.1-12.tgz. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. May I know is there any other approach I can try? Join us at CRISPR workshops in Koper, Slovenia in 2023. Please try reinstalling rlang on a fresh session. To resolve this error, install the required package as a cluster-installed library. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? - the incident has nothing to do with me; can I use this this way? Erasmus+ funds available! In addition: Warning message: I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Start R to confirm they are gone. "After the incident", I started to be more careful not to trip over things. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. privacy statement. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Sounds like there might be an issue with conda setup? How do you ensure that a red herring doesn't violate Chekhov's gun? Does anyone know why I'm getting the following message when I load tidyverse in a new session. R| - Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Then I reinstalled R then Rstudio then RTools. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. [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: Thanks! Is it suspicious or odd to stand by the gate of a GA airport watching the planes? R version 3.6.1 (2019-07-05) Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. As such there are two solutions that may be more or less attainable given your own IT system. Is there anyone the same as mine error while loading library(DESeq2)? Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. 1. When you load the package, you can observe this error. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Solving environment: Found conflicts! 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, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy "4.2") and enter: For older versions of R, please refer to the appropriate "htmlTable", "xfun" I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 More info about Internet Explorer and Microsoft Edge. sessionInfo() [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 What is a word for the arcane equivalent of a monastery? [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 March 1, 2023, 4:56pm library(caret) namespace load failed Object sigma not found caret , . [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 How can I fix error with loading package in R ? | ResearchGate 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: Use of this site constitutes acceptance of our User Agreement and Privacy Is there anything I can do to speed it up? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. I am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. When you load the package, you can observe this error. 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 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"). 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. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Platform: x86_64-apple-darwin15.6.0 (64-bit) I tried again and again was met with missing packages BUT!!! To add to this, I have also been using DESeq2 recently and ran into the same problem. library(DESeq2) C:\R\R-3.4.3\library). there is no package called GenomeInfoDbData [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Update all/some/none? Why do academics stay as adjuncts for years rather than move around? [a/s/n]: A place where magic is studied and practiced? I then launched the R application (from the finder, not RStudio) and installed BiocManager. I tried following the instructions for 2019.7 as well and I am getting the same error. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Solution To resolve this error, install the required package as a cluster-installed library. Did you do that? [7] datasets methods base, other attached packages: The other option is to download and older version of locfit from the package archive and install manually. 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. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: MathJax reference. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Follow Up: struct sockaddr storage initialization by network format-string. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Asking for help, clarification, or responding to other answers. package in your R session. Policy. https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6: https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip', User Agreement and Privacy Why do many companies reject expired SSL certificates as bugs in bug bounties? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Error when installing Aldex2 - Community Plugin Support - Open Source I highly recommend that any R/RStudio version not installed inside conda be removed. Making statements based on opinion; back them up with references or personal experience. Language(R, Python, SQL) DESeq2 installation in R - Bioconductor rev2023.3.3.43278. Why are physically impossible and logically impossible concepts considered separate in terms of probability? to your account. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 If you preorder a special airline meal (e.g. .onLoad failed in loadNamespace() for 'rlang', details: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): If you have a query related to it or one of the replies, start a new topic and refer back with a link. Glad everything is finally working now. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Styling contours by colour and by line thickness in QGIS. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 I've copied the output below in case it helps with troubleshooting.
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