March 1, 2023, 3:25pm March 1, 2023, 4:56pm Not the answer you're looking for? Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Policy. New replies are no longer allowed. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat I just figured Id ask. Have you tried install.packages("locfit") ? Error: package GenomeInfoDb could not be loaded. What do I need to do to reproduce your problem? 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. Platform: x86_64-apple-darwin15.6.0 (64-bit) Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. so I would try to use BiocManager::install("XML"). 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. Convince your IT department to relax the permissions for R packages [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 if (!require("BiocManager", quietly = TRUE)) Thanks! [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 More info about Internet Explorer and Microsoft Edge. How to notate a grace note at the start of a bar with lilypond? [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Sign up for a free GitHub account to open an issue and contact its maintainers and the community. library(DESeq2) 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'. Feedback Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Running under: Windows 10 x64 (build 18362), locale: Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. I even tried BiocManager::install("XML") but all failed as shown below. I hope you can see something I can't see and help me solving this issue. What is a word for the arcane equivalent of a monastery? ERROR: lazy loading failed for package Hmisc Then I reinstalled R then Rstudio then RTools. 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 . To learn more, see our tips on writing great answers. Thank you @hharder. But I guess you have many problems with your installation, and I'd suggest. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. If you try loading the DEseq2 library now, that might work. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? 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. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: 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. 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. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 The best answers are voted up and rise to the top, Not the answer you're looking for? 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. 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. 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. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): This article explains how to resolve the package or namespace loading error. @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. 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 C:\R\R-3.4.3\library). [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 May be the version has problem How can I do ? 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. 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. 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. Open Source Biology & Genetics Interest Group. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc running multiple versions of the same package, keeping separate libraries for some projects). [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 call: dots_list() Running under: macOS Sierra 10.12.6. May I know is there any other approach I can try? Why is this sentence from The Great Gatsby grammatical? Use MathJax to format equations. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Loading required package: GenomeInfoDb R version 4.0.1 (2020-06-06) [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 @artembus Sounds like it was a ton of work! Running. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Looking for incompatible packages.This can take several minutes. This topic was automatically closed 21 days after the last reply. Looking for incompatible packages. 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in enter citation("DESeq2")): To install this package, start R (version Please read the posting [5] IRanges_2.8.1 S4Vectors_0.12.1 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 [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: Should I update the Bioconductor to latest version instead? 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. 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 ERROR: dependency Hmisc is not available for package DESeq2 Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. - the incident has nothing to do with me; can I use this this way? Just realize that I need to write the script "library("DESeq2")" before I proceed. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 R version 3.6.1 (2019-07-05) [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: "htmlTable", "xfun" Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 4. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. (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 . Loading required package: GenomicRanges 1. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR I would recommend installing an older version of QIIME 2 for this plugin to work. I can download DESeq2 using, User Agreement and Privacy To learn more, see our tips on writing great answers. Installation instructions to use this [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 "4.2") and enter: For older versions of R, please refer to the appropriate 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. To view documentation for the version of this package installed Making statements based on opinion; back them up with references or personal experience. privacy statement. By clicking Sign up for GitHub, you agree to our terms of service and By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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). nnet, spatial, survival 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!!! If you have a query related to it or one of the replies, start a new topic and refer back with a link. Is there a proper earth ground point in this switch box? Not the answer you're looking for? Policy. Well occasionally send you account related emails. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 "After the incident", I started to be more careful not to trip over things. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 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. Choose Yes. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): biocLite(), install.packages() (and the devtools equivalent?) Connect and share knowledge within a single location that is structured and easy to search. (Factorization). dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext This can take several minutes. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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 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. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Connect and share knowledge within a single location that is structured and easy to search. to allow custom library locations. [7] datasets methods base, other attached packages: To subscribe to this RSS feed, copy and paste this URL into your RSS reader. After 3-4 manual installs everything worked. Connect and share knowledge within a single location that is structured and easy to search. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. The package has place the R version constraint. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Platform: x86_64-apple-darwin17.0 (64-bit) and then updating the packages that command indicates. Statistics ; Algorithm(ML, DL,.) now when I tried installing the missing packages they did install. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 I also tried something I found on google: but the installation had errors too, I can write them here if needed. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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. 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. library(DESeq2) Start R to confirm they are gone. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Then I reinstalled R then Rstudio then RTools. MathJax reference. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Any other suggestion? However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Making statements based on opinion; back them up with references or personal experience. So if you still get this error try changing your CRAN mirror. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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: Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Disconnect between goals and daily tasksIs it me, or the industry? I installed the package successfully with conda, but Rstudio is apparently does not know about it. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Warning message: Following successful installation of backports BiocManager::install ("DESeq2") will succeed under data . package in your R session. [69] tidyselect_1.0.0. When you load the package, you can observe this error. Are there tables of wastage rates for different fruit and veg? Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. 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. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 That plugin is has not been updated to work with later releases of QIIME 2. there is no package called GenomeInfoDbData C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages To resolve this error, install the required package as a cluster-installed library. 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. 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. install.packages("BiocManager"), I get this error: Also note, however, that the error you got has been associated in the past with mirror outages. March 1, 2023, 8:52pm Find centralized, trusted content and collaborate around the technologies you use most. [7] edgeR_3.16.5 limma_3.30.12 :), BiocManager::install("locift") Why are physically impossible and logically impossible concepts considered separate in terms of probability? Follow Up: struct sockaddr storage initialization by network format-string. .onLoad failed in loadNamespace() for 'rlang', details: How can we prove that the supernatural or paranormal doesn't exist? 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]]): Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) What am I doing wrong here in the PlotLegends specification? Content type 'application/zip' length 386703 bytes (377 KB)