What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Not the answer you're looking for? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? From the console install.packages ("rlang") should fix this. Join us at CRISPR workshops in Koper, Slovenia in 2023. I highly recommend that any R/RStudio version not installed inside conda be removed. How to notate a grace note at the start of a bar with lilypond? Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Installing package(s) 'htmlTable', 'xfun' I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. Did you do that? [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 To resolve this error, install the required package as a cluster-installed library. biocLite(), install.packages() (and the devtools equivalent?) [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Bioconductor release. I can download DESeq2 using, User Agreement and Privacy Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [7] edgeR_3.16.5 limma_3.30.12 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"). Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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 Sorry, I'm newbie. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Policy. 1. 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. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? I've copied the output below in case it helps with troubleshooting. Have a question about this project? In file.copy(savedcopy, lib, recursive = TRUE) : [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Just updated my previous R to 4.01 and now I cant load DESeq2. Thanks for contributing an answer to Bioinformatics Stack Exchange! How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 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. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): package in your R session. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. and then updating the packages that command indicates. March 1, 2023, 3:25pm Error: package GenomeInfoDb could not be loaded. ERROR: dependency Hmisc is not available for package DESeq2 [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Running under: macOS Sierra 10.12.3, locale: If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : March 1, 2023, 7:31pm I am running a new install of R (3.5.0) and RStudio (1.1.414). Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Do I need a thermal expansion tank if I already have a pressure tank? Fortunately I was able to solve it by doing things from several suggested solutions. 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. Have you tried install.packages("locfit") ? 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. March 1, 2023, 8:52pm I hope you can see something I can't see and help me solving this issue. Already on GitHub? Why do academics stay as adjuncts for years rather than move around? This can take several minutes. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Is a PhD visitor considered as a visiting scholar? Platform: x86_64-apple-darwin13.4.0 (64-bit) Find centralized, trusted content and collaborate around the technologies you use most. I do know that it works well in qiime2-2020.6. Sorry if I missed this, the question was quite long so I kind of skimmed, but I noticed that early on some of the packages were reported as requiring manual compilation from source. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). [7] datasets methods base, other attached packages: Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. One solution is to find all available packages. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Why do many companies reject expired SSL certificates as bugs in bug bounties? library(DESeq2) .onLoad failed in loadNamespace() for 'rlang', details: Is there anyone the same as mine error while loading library(DESeq2)? Language(R, Python, SQL) [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. And finally, install the problem packages, perhaps also DESeq2. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib May I know is there any other approach I can try? Making statements based on opinion; back them up with references or personal experience. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 This includes any installed libraries. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages If you try loading the DEseq2 library now, that might work. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 By clicking Sign up for GitHub, you agree to our terms of service and Let me confer with the team. What am I doing wrong here in the PlotLegends specification? Sign in 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. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. 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. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: library(caret) namespace load failed Object sigma not found caret , . If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Erasmus+ funds available! How do you ensure that a red herring doesn't violate Chekhov's gun? + ), update = TRUE, ask = FALSE) I also tried something I found on google: but the installation had errors too, I can write them here if needed. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 The other option is to download and older version of locfit from the package archive and install manually. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Statistics ; Algorithm(ML, DL,.) Use this. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. As such there are two solutions that may be more or less attainable given your own IT system. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Running under: Windows 10 x64 (build 18362), locale: I just figured Id ask. 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. 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 This article explains how to resolve the package or namespace loading error. Making statements based on opinion; back them up with references or personal experience. Feedback Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? It only takes a minute to sign up. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. 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 . sessionInfo() Making statements based on opinion; back them up with references or personal experience. Warning: cannot remove prior installation of package xfun Are you sure the R you're running from the command line is installed through Anaconda as well? Acidity of alcohols and basicity of amines. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Is the God of a monotheism necessarily omnipotent? Policy. Hello, I thought that working in a new environment would help, but it didnt. I tried following the instructions for 2019.7 as well and I am getting the same error. 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. Just realize that I need to write the script "library("DESeq2")" before I proceed. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. package xfun successfully unpacked and MD5 sums checked there is no package called locfit. Not the answer you're looking for? Policy. To learn more, see our tips on writing great answers. Thanks for contributing an answer to Stack Overflow! survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Finally After 3-4 manual installations of missing packages everything worked. Looking for incompatible packages. Learn more about Stack Overflow the company, and our products. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Surly Straggler vs. other types of steel frames. Why is this sentence from The Great Gatsby grammatical? Asking for help, clarification, or responding to other answers. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 No error messages are returned. After 3-4 manual installs everything worked. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( 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 New replies are no longer allowed. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 "4.2") and enter: For older versions of R, please refer to the appropriate 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). unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Please read the posting If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. If you preorder a special airline meal (e.g. Thanks! Solving environment: Found conflicts! "htmlTable", "xfun" Content type 'application/zip' length 233860 bytes (228 KB) Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, To subscribe to this RSS feed, copy and paste this URL into your RSS reader. nnet, spatial, survival Then I reinstalled R then Rstudio then RTools. 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'. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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: Is a PhD visitor considered as a visiting scholar? [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: Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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. Start R to confirm they are gone. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Glad everything is finally working now. R version 4.0.1 (2020-06-06) What do I need to do to reproduce your problem? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [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: 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 [5] IRanges_2.8.1 S4Vectors_0.12.1 So if you still get this error try changing your CRAN mirror. Post questions about Bioconductor Documentation But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () 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 guide. 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. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. binary source needs_compilation enter citation("DESeq2")): To install this package, start R (version Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or? I guess that means we can finally close this issue. 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. 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. Loading required package: GenomeInfoDb Traffic: 307 users visited in the last hour, I am new to all this! Try installing zip, and then loading olsrr. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Running under: macOS Sierra 10.12.6. it would be good to hear any speculation you have of how this might have happened). 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. if (!require("BiocManager", quietly = TRUE)) (Factorization). Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. @artembus Sounds like it was a ton of work! I'm trying to reproduce your problem, so being as precise as possible is important. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 rev2023.3.3.43278. 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. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): sessionInfo() How to use Slater Type Orbitals as a basis functions in matrix method correctly? This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. You signed in with another tab or window. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Running. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Installation instructions to use this Use of this site constitutes acceptance of our User Agreement and Privacy
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