Does anyone know why I'm getting the following message when I load tidyverse in a new session. When an R package depends on a newer package version, the required package is downloaded but not loaded. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Connect and share knowledge within a single location that is structured and easy to search. Use of this site constitutes acceptance of our User Agreement and Privacy [1] stats4 parallel stats graphics grDevices utils Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 (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 . Installing package(s) 'GenomeInfoDbData' Policy. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Running under: Windows 10 x64 (build 18362), locale: 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. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Is there a proper earth ground point in this switch box? Policy. biocLite(), install.packages() (and the devtools equivalent?) If you preorder a special airline meal (e.g. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. @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. If you try loading the DEseq2 library now, that might work. I would recommend installing an older version of QIIME 2 for this plugin to work. Thank you @hharder. it would be good to hear any speculation you have of how this might have happened). Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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. Content type 'application/zip' length 233860 bytes (228 KB) Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) R version 4.0.1 (2020-06-06) Content type 'application/zip' length 386703 bytes (377 KB) Warning message: Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Is there a proper earth ground point in this switch box? Thanks for your suggestion. Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. Platform: x86_64-apple-darwin17.0 (64-bit) [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Finally After 3-4 manual installations of missing packages everything worked. I installed the package successfully with conda, but Rstudio is apparently does not know about it. While a notebook is attached to a cluster, the R namespace cannot be refreshed. So, supposedly the issue is with Hmisc. R version 3.6.3 (2020-02-29) to allow custom library locations. there is no package called locfit. We've tried this - and can replicate this issue on a completely new install with no existing package installs. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Running under: macOS Catalina 10.15.3, Matrix products: default How to use Slater Type Orbitals as a basis functions in matrix method correctly? Well occasionally send you account related emails. Why is this sentence from The Great Gatsby grammatical? 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]]) : [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 there is no package called Hmisc. binary source needs_compilation March 1, 2023, 7:31pm I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Is the God of a monotheism necessarily omnipotent? Hello, 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. I would like to install DESeq2 for DE analysis. Installation instructions to use this 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!!! 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Open Source Biology & Genetics Interest Group. [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. [16] phyloseq1.30.0, loaded via a namespace (and not attached): trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Join us at CRISPR workshops in Koper, Slovenia in 2023. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Use this. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 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. Use MathJax to format equations. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 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 highly recommend that any R/RStudio version not installed inside conda be removed. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( rev2023.3.3.43278. 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: By clicking Sign up for GitHub, you agree to our terms of service and 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. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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: Sounds like there might be an issue with conda setup? Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. sessionInfo() 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. :), BiocManager::install("locift") 4. 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. What is the output of. so I would try to use BiocManager::install("XML"). Sorry, I'm newbie. This includes any installed libraries. If it fails, required operating system facilities are missing. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. What do I need to do to reproduce your problem? I guess that means we can finally close this issue. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' 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. To view documentation for the version of this package installed Making statements based on opinion; back them up with references or personal experience. Why do many companies reject expired SSL certificates as bugs in bug bounties? Should I update the Bioconductor to latest version instead? Update all/some/none? To learn more, see our tips on writing great answers. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. 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. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: I also tried something I found on google: but the installation had errors too, I can write them here if needed. When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. there is no package called data.table Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Whats the grammar of "For those whose stories they are"? Please remember to confirm an answer once you've received one. Error: package GenomeInfoDb could not be loaded. Bad: conda install -c bioconda bioconductor-deseq2. a, There are binary versions available but the source versions are later: That plugin is has not been updated to work with later releases of QIIME 2. And finally, install the problem packages, perhaps also DESeq2. Traffic: 307 users visited in the last hour, I am new to all this! Installing Hmisc as suggested above did not solve the issue. Have a question about this project? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Solution To resolve this error, install the required package as a cluster-installed library. First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). 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). The error states that the current version is 0.4.5 but 0.4.10 is required. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Why is there a voltage on my HDMI and coaxial cables? Loading required package: GenomeInfoDb nnet, spatial, survival Fortunately I was able to solve it by doing things from several suggested solutions. 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. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Asking for help, clarification, or responding to other answers. [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? Running under: macOS Sierra 10.12.6. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. 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. "4.2") and enter: For older versions of R, please refer to the appropriate