Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. nnet, spatial, survival Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib When an R package depends on a newer package version, the required package is downloaded but not loaded. 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"). Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages C:\R\R-3.4.3\library). You are doing something very wrong when installing your packages. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked If not fixed, Try removing remove.packages (rlang) then. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. I was assuming that to be the case. .onLoad failed in loadNamespace() for 'rlang', details: [1] stats4 parallel stats graphics grDevices utils 1. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Is there anything I can do to speed it up? From the console install.packages ("rlang") should fix this. R version 3.6.1 (2019-07-05) and then updating the packages that command indicates. When you load the package, you can observe this error. This can take several minutes. Platform: x86_64-apple-darwin15.6.0 (64-bit) installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Then I reinstalled R then Rstudio then RTools. [69] tidyselect_1.0.0. When you load the package, you can observe this error. Have you tried install.packages("locfit") ? So, supposedly the issue is with Hmisc. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: to allow custom library locations. Sounds like you might have an issue with which R Rstudio is running. binary source needs_compilation problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied, BiocManager::install("XML") Policy. Update all/some/none? /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Powered by Discourse, best viewed with JavaScript enabled, DESeq2: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. What is a word for the arcane equivalent of a monastery? No error messages are returned. Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. @artembus Sounds like it was a ton of work! Installation instructions to use this By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Thanks for contributing an answer to Bioinformatics Stack Exchange! Why are physically impossible and logically impossible concepts considered separate in terms of probability? [13] ggplot23.3.0 car3.0-7 carData3.0-3 Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : + ), update = TRUE, ask = FALSE) [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. Feedback [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Asking for help, clarification, or responding to other answers. library(DESeq2) - the incident has nothing to do with me; can I use this this way? there is no package called locfit. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Running under: macOS Catalina 10.15.3, Matrix products: default nnet, spatial, survival. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: vegan) just to try it, does this inconvenience the caterers and staff? now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Are you sure the R you're running from the command line is installed through Anaconda as well? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Why do academics stay as adjuncts for years rather than move around? Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Already on GitHub? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Retrying with flexible solve.Solving environment: Found conflicts! 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. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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. 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. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Styling contours by colour and by line thickness in QGIS. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Installing package(s) 'htmlTable', 'xfun' Sounds like there might be an issue with conda setup? Please try the following steps: Quit all R/Rstudio sessions. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. To add to this, I have also been using DESeq2 recently and ran into the same problem. Loading required package: GenomeInfoDb 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). [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 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. Is there a proper earth ground point in this switch box? Sign in 2. March 1, 2023, 7:31pm 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 Looking for incompatible packages. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Content type 'application/zip' length 4255589 bytes (4.1 MB) trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Platform: x86_64-w64-mingw32/x64 (64-bit) Acidity of alcohols and basicity of amines. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( to your account. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. R version 4.0.1 (2020-06-06) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Making statements based on opinion; back them up with references or personal experience. so I would try to use BiocManager::install("XML"). 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 . Is there a single-word adjective for "having exceptionally strong moral principles"? Why do academics stay as adjuncts for years rather than move around? Running. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Whats the grammar of "For those whose stories they are"? [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 (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 . Sorry, I'm newbie. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Please remember to confirm an answer once you've received one. Any suggestions would be greatly appreciated. there is no package called data.table Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so That plugin is has not been updated to work with later releases of QIIME 2. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 I'm having a similar error, but different package: library("DESeq2") If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Documentation Content type 'application/zip' length 386703 bytes (377 KB) Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. 4. Warning message: 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. I hope you can see something I can't see and help me solving this issue. Looking for incompatible packages.This can take several minutes. [7] datasets methods base, other attached packages: Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: March 1, 2023, 8:52pm in your system, start R and enter: Follow I thought that working in a new environment would help, but it didnt. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Warning: cannot remove prior installation of package xfun When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. 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 Erasmus+ funds available! What is the output of. Follow Up: struct sockaddr storage initialization by network format-string. there is no package called GenomeInfoDbData sessionInfo() 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 I've copied the output below in case it helps with troubleshooting. The package has place the R version constraint. a, There are binary versions available but the source versions are later: Installing package(s) 'XML' To learn more, see our tips on writing great answers. 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 guess that means we can finally close this issue. Hello, To resolve this error, install the required package as a cluster-installed library. 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]]) : + "htmlTable", "xfun" [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Bioconductor release. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? It is working now. 9. 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. 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 . Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Not the answer you're looking for? I am running a new install of R (3.5.0) and RStudio (1.1.414). C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. I would like to install DESeq2 for DE analysis. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 And finally, install the problem packages, perhaps also DESeq2. This article explains how to resolve the package or namespace loading error. 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. Try again and choose No. [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: More info about Internet Explorer and Microsoft Edge. Policy. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. install.packages ("zip") So if you still get this error try changing your CRAN mirror. Did you do that? [5] IRanges_2.8.1 S4Vectors_0.12.1 Give up and run everything from the "permitted" library location (e.g. ERROR: dependency Hmisc is not available for package DESeq2 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. The error states that the current version is 0.4.5 but 0.4.10 is required. Loading required package: GenomicRanges 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. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Traffic: 307 users visited in the last hour, I am new to all this! C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Replacing broken pins/legs on a DIP IC package. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 I also tried something I found on google: but the installation had errors too, I can write them here if needed. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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. @Tung I've updated my R and RStudio versions (unfortunately I had to first convince my workplace to approve them) and installed the packages through R 3.5.1 however, I'm still getting the same rlang error.
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