Thanks for contributing an answer to Stack Overflow! The error states that the current version is 0.4.5 but 0.4.10 is required. I tried to download the "locfit" package but I can't find it anywhere. Bioconductor - DESeq2 Thanks for contributing an answer to Stack Overflow! .onLoad failed in loadNamespace() for 'rlang', details: sessionInfo() Installation instructions to use this 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. Is the God of a monotheism necessarily omnipotent? The best answers are voted up and rise to the top, Not the answer you're looking for? [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc 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. [1] stats4 parallel stats graphics grDevices utils 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. Platform: x86_64-apple-darwin17.0 (64-bit) Language(R, Python, SQL) [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): What do I need to do to reproduce your problem? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 After 3-4 manual installs everything worked. 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. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Solving environment: Found conflicts! Disconnect between goals and daily tasksIs it me, or the industry? 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 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Glad everything is finally working now. 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) I also tried something I found on google: but the installation had errors too, I can write them here if needed. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. now when I tried installing the missing packages they did install. 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). 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: @artembus Sounds like it was a ton of work! Is there anyone the same as mine error while loading library(DESeq2)? It only takes a minute to sign up. Running under: macOS Catalina 10.15.3, Matrix products: default Any suggestions would be greatly appreciated. Please remember to confirm an answer once you've received one. + ), update = TRUE, ask = FALSE) Citation (from within R, Installing package(s) 'GenomeInfoDbData' Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [7] edgeR_3.16.5 limma_3.30.12 R version 3.6.1 (2019-07-05) + "htmlTable", "xfun" Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 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:\R\R-3.4.3\library). Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Well occasionally send you account related emails. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 March 1, 2023, 7:31pm [16] phyloseq1.30.0, loaded via a namespace (and not attached): Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Why do academics stay as adjuncts for years rather than move around? Use of this site constitutes acceptance of our User Agreement and Privacy Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . 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? rev2023.3.3.43278. there is no package called GenomeInfoDbData Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Start R to confirm they are gone. Platform: x86_64-w64-mingw32/x64 (64-bit) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. (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 . Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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. 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"). Should I update the Bioconductor to latest version instead? More info about Internet Explorer and Microsoft Edge. Policy. 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Warning message: I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Sounds like there might be an issue with conda setup? Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? 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. How to use Slater Type Orbitals as a basis functions in matrix method correctly? Styling contours by colour and by line thickness in QGIS. install.packages ("zip") 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Is a PhD visitor considered as a visiting scholar? This includes any installed libraries. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 The other option is to download and older version of locfit from the package archive and install manually. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Use this. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () R| - 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. Error: package or namespace load failed for 'DESeq2 - Bioconductor 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. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : call: dots_list() Let me confer with the team. Then I reinstalled R then Rstudio then RTools. Erasmus+ funds available! [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Platform: x86_64-apple-darwin13.4.0 (64-bit) [69] tidyselect_1.0.0. I tried following the instructions for 2019.7 as well and I am getting the same error. Is a PhD visitor considered as a visiting scholar? To resolve this error, install the required package as a cluster-installed library. When an R package depends on a newer package version, the required package is downloaded but not loaded. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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. To learn more, see our tips on writing great answers. I am running a new install of R (3.5.0) and RStudio (1.1.414). to your account. 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 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. This topic was automatically closed 21 days after the last reply. Policy. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Looking for incompatible packages.This can take several minutes. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. This article explains how to resolve the package or namespace loading error. package rlang was built under R version 3.5.1. [7] datasets methods base, other attached packages: Making statements based on opinion; back them up with references or personal experience. I even tried BiocManager::install("XML") but all failed as shown below. 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Making statements based on opinion; back them up with references or personal experience. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: library(DESeq2) [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Warning: restored xfun, The downloaded binary packages are in 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. I can download DESeq2 using, User Agreement and Privacy A place where magic is studied and practiced? [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. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 I would recommend installing an older version of QIIME 2 for this plugin to work. there is no package called Hmisc. vegan) just to try it, does this inconvenience the caterers and staff? Have a question about this project? "After the incident", I started to be more careful not to trip over things. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Error when installing Aldex2 - Community Plugin Support - Open Source 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. Why are physically impossible and logically impossible concepts considered separate in terms of probability? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Join us at CRISPR workshops in Koper, Slovenia in 2023. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R.
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