Monat Split End Mender Dupe, Zion Williamson Touching The Top Of The Backboard, Articles E

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]]) : Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Update all/some/none? [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. there is no package called Hmisc. Connect and share knowledge within a single location that is structured and easy to search. I then launched the R application (from the finder, not RStudio) and installed BiocManager. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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. call: dots_list() [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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 Making statements based on opinion; back them up with references or personal experience. This article explains how to resolve the package or namespace loading error. I was assuming that to be the case. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 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? Give up and run everything from the "permitted" library location (e.g. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Warning: cannot remove prior installation of package xfun Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Error: package GenomeInfoDb could not be loaded. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Acidity of alcohols and basicity of amines. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in I thought that working in a new environment would help, but it didnt. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Is there anything I can do to speed it up? Running under: macOS Sierra 10.12.6. 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. Not the answer you're looking for? How to use Slater Type Orbitals as a basis functions in matrix method correctly? 1. Solving environment: Found conflicts! By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. to your account. [1] stats4 parallel stats graphics grDevices utils However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 [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: 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. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Running under: macOS Catalina 10.15.3, Matrix products: default Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. The other option is to download and older version of locfit from the package archive and install manually. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Solution To resolve this error, install the required package as a cluster-installed library. The package has place the R version constraint. After 3-4 manual installs everything worked. 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. 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). 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: R version 3.6.3 (2020-02-29) [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 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. More info about Internet Explorer and Microsoft Edge. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Any other suggestion? Thanks for your suggestion. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): guide. Well occasionally send you account related emails. 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: What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc March 1, 2023, 4:56pm 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. I installed the package successfully with conda, but Rstudio is apparently does not know about it. 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. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Making statements based on opinion; back them up with references or personal experience. Is a PhD visitor considered as a visiting scholar? If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Platform: x86_64-w64-mingw32/x64 (64-bit) [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. How do I align things in the following tabular environment? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 + "htmlTable", "xfun" in your system, start R and enter: Follow Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) If you preorder a special airline meal (e.g. 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. Post questions about Bioconductor 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? library(DESeq2) LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: March 1, 2023, 8:52pm I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Finally After 3-4 manual installations of missing packages everything worked. But I guess you have many problems with your installation, and I'd suggest. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Find centralized, trusted content and collaborate around the technologies you use most. When an R package depends on a newer package version, the required package is downloaded but not loaded. Warning: restored xfun, The downloaded binary packages are in rev2023.3.3.43278. a, There are binary versions available but the source versions are later: [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Is a PhD visitor considered as a visiting scholar? there is no package called locfit. Platform: x86_64-apple-darwin15.6.0 (64-bit) "4.2") and enter: For older versions of R, please refer to the appropriate Why do many companies reject expired SSL certificates as bugs in bug bounties? [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Just updated my previous R to 4.01 and now I cant load DESeq2. Is the God of a monotheism necessarily omnipotent? Have a question about this project? [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 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. Running. :), BiocManager::install("locift") library(DESeq2) Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Open Source Biology & Genetics Interest Group. there is no package called GenomeInfoDbData [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Thanks for contributing an answer to Stack Overflow! [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 How to notate a grace note at the start of a bar with lilypond? Erasmus+ funds available! RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE vegan) just to try it, does this inconvenience the caterers and staff? [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 May I know is there any other approach I can try? running multiple versions of the same package, keeping separate libraries for some projects). Policy. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Thank you @hharder. Policy. Is there anyone the same as mine error while loading library(DESeq2)? Loading required package: GenomicRanges [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): If you try loading the DEseq2 library now, that might work. 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. I tried following the instructions for 2019.7 as well and I am getting the same error. How do you ensure that a red herring doesn't violate Chekhov's gun? Use of this site constitutes acceptance of our User Agreement and Privacy Citation (from within R, Content type 'application/zip' length 386703 bytes (377 KB) Installation instructions to use this Remember to always click on the red Show me the content on this page notice when navigating these older versions. 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. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. 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. Are you sure the R you're running from the command line is installed through Anaconda as well? 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. What am I doing wrong here in the PlotLegends specification? Policy. So, supposedly the issue is with Hmisc. Installing Hmisc as suggested above did not solve the issue. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Learn more about Stack Overflow the company, and our products. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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 Old packages: 'RcppArmadillo', 'survival' The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Press CTRL-C to abort. 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. The error states that the current version is 0.4.5 but 0.4.10 is required. 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. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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). [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Warning message: To add to this, I have also been using DESeq2 recently and ran into the same problem. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [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. Please try reinstalling rlang on a fresh session. so I would try to use BiocManager::install("XML"). 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 C:\R\R-3.4.3\library). Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Sounds like you might have an issue with which R Rstudio is running. Use this. 2. 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. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked rev2023.3.3.43278. install.packages ("zip") package xfun successfully unpacked and MD5 sums checked [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. From the console install.packages ("rlang") should fix this. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Feedback Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. Start R to confirm they are gone. Then I reinstalled R then Rstudio then RTools. Language(R, Python, SQL) I'm having a similar error, but different package: library("DESeq2") Sorry, I'm newbie. It is working now. May be the version has problem How can I do ? I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Why is this sentence from The Great Gatsby grammatical? - the incident has nothing to do with me; can I use this this way? March 1, 2023, 7:31pm 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: 9. Making statements based on opinion; back them up with references or personal experience.