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: Have a question about this project? I have tried your suggestion and also updating the packages that command indicates. package rlang was built under R version 3.5.1. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R After 3-4 manual installs everything worked. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? To add to this, I have also been using DESeq2 recently and ran into the same problem. Browse other questions tagged, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site. March 1, 2023, 3:25pm I hope you can see something I can't see and help me solving this issue. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 I also tried something I found on google: but the installation had errors too, I can write them here if needed. 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) I would recommend installing an older version of QIIME 2 for this plugin to work. I can download DESeq2 using, User Agreement and Privacy If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : 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. Any suggestions would be greatly appreciated. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. so I would try to use BiocManager::install("XML"). Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? This is the beauty of installing QIIME 2 via conda, you can have many different versions of QIIME 2 on your system at the same time and activate the version you want to use. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 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 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Convince your IT department to relax the permissions for R packages to allow custom library locations. ERROR: lazy loading failed for package Hmisc "After the incident", I started to be more careful not to trip over things. library(caret) namespace load failed Object sigma not found caret , . RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE 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 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Do I need a thermal expansion tank if I already have a pressure tank? I installed the package successfully with conda, but Rstudio is apparently does not know about it. C:\R\R-3.4.3\library). What do I need to do to reproduce your problem? The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? To learn more, see our tips on writing great answers. From the console install.packages ("rlang") should fix this. I highly recommend that any R/RStudio version not installed inside conda be removed. 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. library(DESeq2) 9. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 Platform: x86_64-apple-darwin15.6.0 (64-bit) [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Just to add on -- do you require an old version of Bioconductor for your current project? Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. The other option is to download and older version of locfit from the package archive and install manually. Platform: x86_64-apple-darwin17.0 (64-bit) Connect and share knowledge within a single location that is structured and easy to search. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Learn more about Stack Overflow the company, and our products. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 + "htmlTable", "xfun" * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. "htmlTable", "xfun" To view documentation for the version of this package installed (Factorization). Warning message: Whats the grammar of "For those whose stories they are"? Solving environment: Found conflicts! Content type 'application/zip' length 386703 bytes (377 KB) 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). running multiple versions of the same package, keeping separate libraries for some projects). The best answers are voted up and rise to the top, Not the answer you're looking for? nnet, spatial, survival. Thanks! In addition: Warning message: May be the version has problem How can I do ? 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!!! Sorry, I'm newbie. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 I guess that means we can finally close this issue. Any other suggestion? The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. [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: BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib MathJax reference. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Join us at CRISPR workshops in Koper, Slovenia in 2023. 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. 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. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 May I know is there any other approach I can try? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) The error states that the current version is 0.4.5 but 0.4.10 is required. Please remember to confirm an answer once you've received one. Please try the following steps: Quit all R/Rstudio sessions. Solution To resolve this error, install the required package as a cluster-installed library. Thanks for your suggestion. Surly Straggler vs. other types of steel frames. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Sign in installation of package GenomeInfoDbData had non-zero exit status. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. How can we prove that the supernatural or paranormal doesn't exist? [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 data . [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: We've tried this - and can replicate this issue on a completely new install with no existing package installs. Try installing zip, and then loading olsrr. Installing package(s) 'XML' It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Feedback Warning: restored xfun, The downloaded binary packages are in Platform: x86_64-apple-darwin13.4.0 (64-bit) My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Did you do that? I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Looking for incompatible packages.This can take several minutes. 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'. Error: package GenomeInfoDb could not be loaded. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Also make sure that you have RTools.exe installed and working. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. R version 3.6.1 (2019-07-05) I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in How do I align things in the following tabular environment? Installing package(s) 'htmlTable', 'xfun' biocLite(), install.packages() (and the devtools equivalent?) Policy. To resolve this error, install the required package as a cluster-installed library. 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"). Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Is the God of a monotheism necessarily omnipotent? Installing Hmisc as suggested above did not solve the issue. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Documentation Use MathJax to format equations. Content type 'application/zip' length 233860 bytes (228 KB) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [7] edgeR_3.16.5 limma_3.30.12 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 Thnaks anyway, Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems, How Intuit democratizes AI development across teams through reusability. Running under: Windows 10 x64 (build 18362), locale: Why do academics stay as adjuncts for years rather than move around? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' @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. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Is a PhD visitor considered as a visiting scholar? This includes any installed libraries. So, supposedly the issue is with Hmisc. Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 sessionInfo() By clicking Sign up for GitHub, you agree to our terms of service and rev2023.3.3.43278. Already on GitHub? Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. I then launched the R application (from the finder, not RStudio) and installed BiocManager. I just figured Id ask. [7] datasets methods base, other attached packages: privacy statement. :), BiocManager::install("locift") Warning message: A place where magic is studied and practiced? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. package in your R session. [a/s/n]: 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). You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Update all/some/none? To learn more, see our tips on writing great answers. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Well occasionally send you account related emails. What is a word for the arcane equivalent of a monastery? How to notate a grace note at the start of a bar with lilypond? 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. @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. [5] IRanges_2.8.1 S4Vectors_0.12.1 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. 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 . 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. 2. This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. - the incident has nothing to do with me; can I use this this way? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Looking for incompatible packages. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 When you load the package, you can observe this error. Policy. Warning: cannot remove prior installation of package xfun ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: 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"). 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. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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 [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [69] tidyselect_1.0.0. [1] stats4 parallel stats graphics grDevices utils downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 in your system, start R and enter: Follow [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 . 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. I thought that working in a new environment would help, but it didnt. Is there a proper earth ground point in this switch box? 4. I even tried BiocManager::install("XML") but all failed as shown below. I do know that it works well in qiime2-2020.6. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? This can take several minutes. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat 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 .