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. I tried to download the "locfit" package but I can't find it anywhere. I do know that it works well in qiime2-2020.6. Platform: x86_64-apple-darwin17.0 (64-bit) if (!require("BiocManager", quietly = TRUE)) Sorry, I'm newbie. Thanks for your 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. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Styling contours by colour and by line thickness in QGIS. I even tried BiocManager::install("XML") but all failed as shown below. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so What am I doing wrong here in the PlotLegends specification? After 3-4 manual installs everything worked. Installing package(s) 'GenomeInfoDbData' Replacing broken pins/legs on a DIP IC package. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 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. [7] datasets methods base, other attached packages: New replies are no longer allowed. 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. Is the God of a monotheism necessarily omnipotent? Bad: conda install -c bioconda bioconductor-deseq2. In install.packages() : DESeq2_2301_76497647-CSDN Press CTRL-C to abort. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 + ), update = TRUE, ask = FALSE) [1] stats4 parallel stats graphics grDevices utils [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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'. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Just updated my previous R to 4.01 and now I cant load DESeq2. Solving environment: Found conflicts! [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Thanks for contributing an answer to Bioinformatics Stack Exchange! [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Sounds like you might have an issue with which R Rstudio is running. [40] assertthat_0.1 rpart_4.1-10 nnet_7.3-12, It should not be necessary (R should take care of loading dependencies) but try installating data.table also. Join us at CRISPR workshops in Koper, Slovenia in 2023. Well occasionally send you account related emails. I have tried your suggestion and also updating the packages that command indicates. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? May be the version has problem How can I do ? 4. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Warning: cannot remove prior installation of package xfun Thanks for contributing an answer to Stack Overflow! + "htmlTable", "xfun" Platform: x86_64-apple-darwin15.6.0 (64-bit) If you have a query related to it or one of the replies, start a new topic and refer back with a link. 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? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. As such there are two solutions that may be more or less attainable given your own IT system. Finally After 3-4 manual installations of missing packages everything worked. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 To learn more, see our tips on writing great answers. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. rev2023.3.3.43278. there is no package called Hmisc. A place where magic is studied and practiced? I've copied the output below in case it helps with troubleshooting. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [13] ggplot23.3.0 car3.0-7 carData3.0-3 Have you tried install.packages("locfit") ? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): When an R package depends on a newer package version, the required package is downloaded but not loaded. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Thank you @hharder. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. 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). install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Please remember to confirm an answer once you've received one. One solution is to find all available packages. Citation (from within R, Remember to always click on the red Show me the content on this page notice when navigating these older versions. 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. Policy. now when I tried installing the missing packages they did install. If it fails, required operating system facilities are missing. Use of this site constitutes acceptance of our User Agreement and Privacy .onLoad failed in loadNamespace() for 'rlang', details: Please try the following steps: Quit all R/Rstudio sessions. Surly Straggler vs. other types of steel frames. [a/s/n]: I hope you can see something I can't see and help me solving this issue. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages To learn more, see our tips on writing great answers. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 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. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 So, supposedly the issue is with Hmisc. Solution To resolve this error, install the required package as a cluster-installed library. 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. I guess that means we can finally close this issue. Whats the grammar of "For those whose stories they are"? library(DESeq2) By clicking Sign up for GitHub, you agree to our terms of service and Should I update the Bioconductor to latest version instead? 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! I also tried something I found on google: but the installation had errors too, I can write them here if needed. I'm having a similar error, but different package: library("DESeq2") As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. Learn more about Stack Overflow the company, and our products. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 ()library(DESeq2):Error in loadNamespace: no package called ""s 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. Why is this sentence from The Great Gatsby grammatical? there is no package called 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. How do I align things in the following tabular environment? nnet, spatial, survival 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. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Follow Up: struct sockaddr storage initialization by network format-string. 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 . [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Erasmus+ funds available! Is a PhD visitor considered as a visiting scholar? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Use MathJax to format equations. running multiple versions of the same package, keeping separate libraries for some projects). 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 data . 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. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Installing package(s) 'XML' The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: @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-darwin13.4.0 (64-bit) Find centralized, trusted content and collaborate around the technologies you use most. - the incident has nothing to do with me; can I use this this way? How to use Slater Type Orbitals as a basis functions in matrix method correctly? MathJax reference. 1. I can download DESeq2 using, User Agreement and Privacy installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Resolving package or namespace loading error Sign in 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. How can we prove that the supernatural or paranormal doesn't exist? What is the output of. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? If you try loading the DEseq2 library now, that might work. call: dots_list() You signed in with another tab or window. Start R to confirm they are gone. Installing Hmisc as suggested above did not solve the issue. Fortunately I was able to solve it by doing things from several suggested solutions. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Language(R, Python, SQL) Install DESeq2 through anaconda - Bioinformatics Stack Exchange To subscribe to this RSS feed, copy and paste this URL into your RSS reader. sessionInfo() Running. Retrying with flexible solve.Solving environment: Found conflicts! Is a PhD visitor considered as a visiting scholar? there is no package called GenomeInfoDbData * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc 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 in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) library (olsrr) - Error - General - RStudio Community This can take several minutes. No error messages are returned. Disconnect between goals and daily tasksIs it me, or the industry? And finally, install the problem packages, perhaps also DESeq2. R version 4.0.1 (2020-06-06) Just realize that I need to write the script "library("DESeq2")" before I proceed. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. March 1, 2023, 8:52pm Also note, however, that the error you got has been associated in the past with mirror outages. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked 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. 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. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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"). Loading required package: GenomeInfoDb Thanks! [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. March 1, 2023, 4:56pm 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") From the console install.packages ("rlang") should fix this. library(caret) namespace load failed Object sigma not ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR I was assuming that to be the case. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 I thought that working in a new environment would help, but it didnt. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Post questions about Bioconductor Policy. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Content type 'application/zip' length 4255589 bytes (4.1 MB) I installed the package successfully with conda, but Rstudio is apparently does not know about it. Bioconductor release. 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. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. Rload failed - [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 I want to import DESeq2 in Rstudio though and it is giving me a different error when I try importing DESeq2: Error in library("DESeq2") : there is no package called DESeq2. so I would try to use BiocManager::install("XML"). Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Documentation If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. library(caret) namespace load failed Object sigma not found caret , . Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub 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 installation of package GenomeInfoDbData had non-zero exit status. (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 . Is there anyone the same as mine error while loading library(DESeq2)? Making statements based on opinion; back them up with references or personal experience. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Hello, Is there a proper earth ground point in this switch box? [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 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. When you load the package, you can observe this error. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Making statements based on opinion; back them up with references or personal experience. a, There are binary versions available but the source versions are later: error: object 'rlang_dots_list' not found Connect and share knowledge within a single location that is structured and easy to search. 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: 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 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R @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. Policy. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [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: 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. Warning message: [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 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"). To resolve this error, install the required package as a cluster-installed library. [7] edgeR_3.16.5 limma_3.30.12 It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. 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. 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'. 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]]): R version 3.6.3 (2020-02-29) I'm trying to reproduce your problem, so being as precise as possible is important. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 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. [5] IRanges_2.8.1 S4Vectors_0.12.1 Statistics ; Algorithm(ML, DL,.) Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat This includes any installed libraries. Why are physically impossible and logically impossible concepts considered separate in terms of probability? sessionInfo() I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu.