installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat How can we prove that the supernatural or paranormal doesn't exist? [7] datasets methods base, other attached packages: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc March 1, 2023, 7:31pm This topic was automatically closed 21 days after the last reply. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Why do academics stay as adjuncts for years rather than move around? Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Content type 'application/zip' length 4255589 bytes (4.1 MB) 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 Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. @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. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): [13] ggplot23.3.0 car3.0-7 carData3.0-3 to allow custom library locations. 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. 4. 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. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 if (!require("BiocManager", quietly = TRUE)) You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 You signed in with another tab or window. Connect and share knowledge within a single location that is structured and easy to search. MathJax reference. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Use this. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 in your system, start R and enter: Follow But I guess you have many problems with your installation, and I'd suggest. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. 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. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Is there a proper earth ground point in this switch box? 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"). Press CTRL-C to abort. rev2023.3.3.43278. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 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. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Content type 'application/zip' length 386703 bytes (377 KB) Are you sure the R you're running from the command line is installed through Anaconda as well? I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Solving environment: Found conflicts! The best answers are voted up and rise to the top, Not the answer you're looking for? R version 3.6.3 (2020-02-29) If not fixed, Try removing remove.packages (rlang) then. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Join us at CRISPR workshops in Koper, Slovenia in 2023. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, + ), update = TRUE, ask = FALSE) I hope you can see something I can't see and help me solving this issue. I even tried BiocManager::install("XML") but all failed as shown below. That plugin is has not been updated to work with later releases of QIIME 2. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. 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]]) : C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. there is no package called locfit. I'm trying to reproduce your problem, so being as precise as possible is important. [7] edgeR_3.16.5 limma_3.30.12 Making statements based on opinion; back them up with references or personal experience. 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. [5] IRanges_2.8.1 S4Vectors_0.12.1 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. @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. Platform: x86_64-apple-darwin17.0 (64-bit) Installing package(s) 'htmlTable', 'xfun' Loading required package: GenomicRanges 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. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Policy. Loading required package: GenomeInfoDb Running under: Windows 10 x64 (build 18362), locale: A place where magic is studied and practiced? Use of this site constitutes acceptance of our User Agreement and Privacy 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: Erasmus+ funds available! Any suggestions would be greatly appreciated. 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'. 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 . Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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. it would be good to hear any speculation you have of how this might have happened). How to notate a grace note at the start of a bar with lilypond? Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. [a/s/n]: [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Why do many companies reject expired SSL certificates as bugs in bug bounties? Not the answer you're looking for? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). library(caret) namespace load failed Object sigma not found caret , . 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. When you load the package, you can observe this error. Platform: x86_64-apple-darwin13.4.0 (64-bit) Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. there is no package called GenomeInfoDbData trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Are there tables of wastage rates for different fruit and veg? * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. 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 I then launched the R application (from the finder, not RStudio) and installed BiocManager. Connect and share knowledge within a single location that is structured and easy to search. Replacing broken pins/legs on a DIP IC package. package rlang was built under R version 3.5.1. 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. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 In install.packages() : Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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). [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 sessionInfo() Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 How do you ensure that a red herring doesn't violate Chekhov's gun? 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. Do I need a thermal expansion tank if I already have a pressure tank? I tried following the instructions for 2019.7 as well and I am getting the same error. Making statements based on opinion; back them up with references or personal experience. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: To view documentation for the version of this package installed Why are physically impossible and logically impossible concepts considered separate in terms of probability? [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Policy. 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. While a notebook is attached to a cluster, the R namespace cannot be refreshed. enter citation("DESeq2")): To install this package, start R (version I also tried something I found on google: but the installation had errors too, I can write them here if needed. Let me confer with the team. 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. - the incident has nothing to do with me; can I use this this way? RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 9. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. As such there are two solutions that may be more or less attainable given your own IT system. nnet, spatial, survival. 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. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. running multiple versions of the same package, keeping separate libraries for some projects). 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. 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. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () When an R package depends on a newer package version, the required package is downloaded but not loaded. R version 4.0.1 (2020-06-06) Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Also note, however, that the error you got has been associated in the past with mirror outages. Installing package(s) 'GenomeInfoDbData' March 1, 2023, 8:52pm 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: Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Looking for incompatible packages.This can take several minutes. It only takes a minute to sign up. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Glad everything is finally working now. there is no package called data.table Did you do that? Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Asking for help, clarification, or responding to other answers. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. This includes any installed libraries. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Documentation :), BiocManager::install("locift") However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Installation instructions to use this Post questions about Bioconductor The package has place the R version constraint. If it fails, required operating system facilities are missing. Try installing zip, and then loading olsrr. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. Just to add on -- do you require an old version of Bioconductor for your current project? and then updating the packages that command indicates. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Citation (from within R, Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. I have tried your suggestion and also updating the packages that command indicates. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 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 im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. R version 3.6.1 (2019-07-05) How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Running under: macOS Catalina 10.15.3, Matrix products: default Why do academics stay as adjuncts for years rather than move around? Sorry, I'm newbie. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Use of this site constitutes acceptance of our User Agreement and Privacy 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") 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. 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. Making statements based on opinion; back them up with references or personal experience. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib 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. What do I need to do to reproduce your problem? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 May be the version has problem How can I do ? Fortunately I was able to solve it by doing things from several suggested solutions. installation of package GenomeInfoDbData had non-zero exit status. Update all/some/none? Thanks for contributing an answer to Stack Overflow! rev2023.3.3.43278. there is no package called Hmisc. install.packages("BiocManager"), I get this error: Why is there a voltage on my HDMI and coaxial cables? Traffic: 307 users visited in the last hour, I am new to all this! package xfun successfully unpacked and MD5 sums checked More info about Internet Explorer and Microsoft Edge. privacy statement. Disconnect between goals and daily tasksIs it me, or the industry? Open Source Biology & Genetics Interest Group. In addition: Warning message: Just realize that I need to write the script "library("DESeq2")" before I proceed. Sounds like you might have an issue with which R Rstudio is running. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 I'm having a similar error, but different package: library("DESeq2") I am running a new install of R (3.5.0) and RStudio (1.1.414). [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 I just figured Id ask. 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: [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 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. Already on GitHub? [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 call: dots_list() Learn more about Stack Overflow the company, and our products. To learn more, see our tips on writing great answers. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . 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!!! [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: 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. so I would try to use BiocManager::install("XML"). Styling contours by colour and by line thickness in QGIS. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated.
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