Why is this sentence from The Great Gatsby grammatical? Whats the grammar of "For those whose stories they are"? dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 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. 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: [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 vegan) just to try it, does this inconvenience the caterers and staff? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Styling contours by colour and by line thickness in QGIS. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. (Factorization). I tried following the instructions for 2019.7 as well and I am getting the same error. Also make sure that you have RTools.exe installed and working. 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. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Installing Hmisc as suggested above did not solve the issue. Policy. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? there is no package called GenomeInfoDbData Running under: Windows 10 x64 (build 18362), locale: I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. package xfun successfully unpacked and MD5 sums checked I highly recommend that any R/RStudio version not installed inside conda be removed. biocLite(), install.packages() (and the devtools equivalent?) library(caret) namespace load failed Object sigma not found caret , . 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. Update all/some/none? error: object 'rlang_dots_list' not found + "htmlTable", "xfun" So, supposedly the issue is with Hmisc. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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'. Why do academics stay as adjuncts for years rather than move around? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. there is no package called locfit. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Remember to always click on the red Show me the content on this page notice when navigating these older versions. 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. I just figured Id ask. It only takes a minute to sign up. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. "htmlTable", "xfun" The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Is a PhD visitor considered as a visiting scholar? .onLoad failed in loadNamespace() for 'rlang', details: nnet, spatial, survival. In file.copy(savedcopy, lib, recursive = TRUE) : Just to add on -- do you require an old version of Bioconductor for your current project? From the console install.packages ("rlang") should fix this. March 1, 2023, 7:31pm This topic was automatically closed 21 days after the last reply. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Platform: x86_64-w64-mingw32/x64 (64-bit) Warning message: [7] edgeR_3.16.5 limma_3.30.12 - the incident has nothing to do with me; can I use this this way? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so No error messages are returned. 9. Just realize that I need to write the script "library("DESeq2")" before I proceed. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Just updated my previous R to 4.01 and now I cant load DESeq2. 4. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 2. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. install.packages ("zip") What do I need to do to reproduce your problem? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under to your account. I would like to install DESeq2 for DE analysis. 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. Please read the posting Loading required package: GenomicRanges 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. Surly Straggler vs. other types of steel frames. 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 Try again and choose No. Making statements based on opinion; back them up with references or personal experience. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Fortunately I was able to solve it by doing things from several suggested solutions. Content type 'application/zip' length 4255589 bytes (4.1 MB) 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: @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. After 3-4 manual installs everything worked. 1. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. What is the output of. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: Making statements based on opinion; back them up with references or personal experience. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [16] phyloseq1.30.0, loaded via a namespace (and not attached): Is a PhD visitor considered as a visiting scholar? Find centralized, trusted content and collaborate around the technologies you use most. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. You signed in with another tab or window. Use of this site constitutes acceptance of our User Agreement and Privacy Well occasionally send you account related emails. 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. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: I've copied the output below in case it helps with troubleshooting. 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. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): The error states that the current version is 0.4.5 but 0.4.10 is required. 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!!! Convince your IT department to relax the permissions for R packages I have tried your suggestion and also updating the packages that command indicates. nnet, spatial, survival One solution is to find all available packages. Looking for incompatible packages. there is no package called Hmisc. data . Open Source Biology & Genetics Interest Group. Sounds like you might have an issue with which R Rstudio is running. 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). /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages 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. Solving environment: Found conflicts! 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. Give up and run everything from the "permitted" library location (e.g. Then I reinstalled R then Rstudio then RTools. package rlang was built under R version 3.5.1. 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. "After the incident", I started to be more careful not to trip over things. Thanks! So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. 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. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' And finally, install the problem packages, perhaps also DESeq2. "After the incident", I started to be more careful not to trip over things. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 [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: [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 there is no package called data.table downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Platform: x86_64-apple-darwin15.6.0 (64-bit) ERROR: dependency Hmisc is not available for package DESeq2 I do know that it works well in qiime2-2020.6. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 library(DESeq2) 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. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. package in your R session. How do you ensure that a red herring doesn't violate Chekhov's gun? The package has place the R version constraint. 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. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Old packages: 'RcppArmadillo', 'survival' I then launched the R application (from the finder, not RStudio) and installed BiocManager. Why is there a voltage on my HDMI and coaxial cables? ERROR: lazy loading failed for package Hmisc Looking for incompatible packages.This can take several minutes. 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. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Then I reinstalled R then Rstudio then RTools. 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 . Statistics ; Algorithm(ML, DL,.) 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. . [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 R version 4.0.1 (2020-06-06) Warning: restored xfun, The downloaded binary packages are in Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Are you sure the R you're running from the command line is installed through Anaconda as well? Connect and share knowledge within a single location that is structured and easy to search. Sign in 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. Is there a proper earth ground point in this switch box? 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'. How do I align things in the following tabular environment? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I can download DESeq2 using, User Agreement and Privacy Running under: macOS Sierra 10.12.3, locale: Should I update the Bioconductor to latest version instead? Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? I thought that working in a new environment would help, but it didnt. to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. Use this. Any other suggestion? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Join us at CRISPR workshops in Koper, Slovenia in 2023. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 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. To learn more, see our tips on writing great answers. 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. it would be good to hear any speculation you have of how this might have happened). Installation instructions to use this March 1, 2023, 4:56pm Error: package GenomeInfoDb could not be loaded. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? To learn more, see our tips on writing great answers. call: dots_list() running multiple versions of the same package, keeping separate libraries for some projects). If you have a query related to it or one of the replies, start a new topic and refer back with a link. 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. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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. This can take several minutes. You are doing something very wrong when installing your packages. + ), update = TRUE, ask = FALSE) Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Thanks for contributing an answer to Stack Overflow! [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 In addition: Warning message: I was assuming that to be the case. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. I'm having a similar error, but different package: library("DESeq2") Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Traffic: 307 users visited in the last hour, I am new to all this! Why do academics stay as adjuncts for years rather than move around? Is the God of a monotheism necessarily omnipotent? [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Connect and share knowledge within a single location that is structured and easy to search. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Policy. [5] IRanges_2.8.1 S4Vectors_0.12.1 How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? How can we prove that the supernatural or paranormal doesn't exist? [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 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. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Use of this site constitutes acceptance of our User Agreement and Privacy March 1, 2023, 3:25pm I'd take a look at need, to see if there are any insights to be had, so that you can correct the root problem rather than having to do this procedure with other packages. Now loading the DESeq2 library (Errors): Because I already installed >10 packages by hand I assume the solution is not to keep installing the missing packages because those packages will have more missing packages and more and more and I won't get out of this loop. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib The best answers are voted up and rise to the top, Not the answer you're looking for? binary source needs_compilation [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3