[34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': ()library(DESeq2):Error in loadNamespace: no package called ""s To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 When you load the package, you can observe this error. Thanks! Platform: x86_64-apple-darwin15.6.0 (64-bit) Try again and choose No. :), BiocManager::install("locift") install.packages("BiocManager"), I get this error: I then launched the R application (from the finder, not RStudio) and installed BiocManager. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Let me confer with the team. Connect and share knowledge within a single location that is structured and easy to search. Making statements based on opinion; back them up with references or personal experience. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 [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. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Policy. To learn more, see our tips on writing great answers. Surly Straggler vs. other types of steel frames. Loading required package: GenomeInfoDb rev2023.3.3.43278. One solution is to find all available packages. This includes any installed libraries. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 9. Sign in Glad everything is finally working now. Asking for help, clarification, or responding to other answers. Running under: macOS Sierra 10.12.3, locale: Hello, Use of this site constitutes acceptance of our User Agreement and Privacy 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. Update all/some/none? Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . In file.copy(savedcopy, lib, recursive = TRUE) : 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. Statistics ; Algorithm(ML, DL,.) R version 4.0.1 (2020-06-06) biocLite(), install.packages() (and the devtools equivalent?) Making statements based on opinion; back them up with references or personal experience. I just figured Id ask. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' . More info about Internet Explorer and Microsoft Edge. That plugin is has not been updated to work with later releases of QIIME 2. 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. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. R version 3.6.3 (2020-02-29) How do you ensure that a red herring doesn't violate Chekhov's gun? How can we prove that the supernatural or paranormal doesn't exist? enter citation("DESeq2")): To install this package, start R (version How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? [69] tidyselect_1.0.0. 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 0 packages out-of-date; 2 packages too new, BiocManager::install(c( 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. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' 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 Have a question about this project? And finally, install the problem packages, perhaps also DESeq2. Sounds like there might be an issue with conda setup? The error states that the current version is 0.4.5 but 0.4.10 is required. 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 . Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): So if you still get this error try changing your CRAN mirror. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( sessionInfo() Are you sure the R you're running from the command line is installed through Anaconda as well? [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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'. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 The package has place the R version constraint. Error: package or namespace load failed, object not found Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Please read the posting Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I was assuming that to be the case. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. R DESeq2 - library(DESeq2) Is there anything I can do to speed it up? [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 I would like to install DESeq2 for DE analysis. 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. If not fixed, Try removing remove.packages (rlang) then. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Content type 'application/zip' length 386703 bytes (377 KB) there is no package called locfit. What do I need to do to reproduce your problem? This topic was automatically closed 21 days after the last reply. After 3-4 manual installs everything worked. Any other suggestion? there is no package called data.table now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Find centralized, trusted content and collaborate around the technologies you use most. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: By clicking Sign up for GitHub, you agree to our terms of service and To add to this, I have also been using DESeq2 recently and ran into the same problem. there is no package called Hmisc. [a/s/n]: [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 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 . 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") guide. + ), update = TRUE, ask = FALSE) May be the version has problem How can I do ? LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: 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. I have tried your suggestion and also updating the packages that command indicates. a, There are binary versions available but the source versions are later: 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. Platform: x86_64-w64-mingw32/x64 (64-bit) Do I need a thermal expansion tank if I already have a pressure tank? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Thanks for contributing an answer to Bioinformatics Stack Exchange! [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Resolving package or namespace loading error May I know is there any other approach I can try? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Running under: Windows 10 x64 (build 18362), locale: [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 What is a word for the arcane equivalent of a monastery? Platform: x86_64-apple-darwin13.4.0 (64-bit) Whats the grammar of "For those whose stories they are"? What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. 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. I'm trying to reproduce your problem, so being as precise as possible is important. New replies are no longer allowed. package rlang was built under R version 3.5.1. Is there a proper earth ground point in this switch box? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. .onLoad failed in loadNamespace() for 'rlang', details: 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'. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : 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"). As such there are two solutions that may be more or less attainable given your own IT system. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Also make sure that you have RTools.exe installed and working. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. This can take several minutes. Thanks for contributing an answer to Stack Overflow! I'm having a similar error, but different package: library("DESeq2") Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Citation (from within R, DESeq2_2301_76497647-CSDN Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) The best answers are voted up and rise to the top, Not the answer you're looking for? ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR in your system, start R and enter: Follow @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. 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: Why is this sentence from The Great Gatsby grammatical? Retrying with flexible solve.Solving environment: Found conflicts! Post questions about Bioconductor Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc I tried to download the "locfit" package but I can't find it anywhere. Disconnect between goals and daily tasksIs it me, or the industry? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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. binary source needs_compilation Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Also note, however, that the error you got has been associated in the past with mirror outages. ERROR: dependency Hmisc is not available for package DESeq2 Thanks for your suggestion. 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]]): Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): running multiple versions of the same package, keeping separate libraries for some projects). Is a PhD visitor considered as a visiting scholar? * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. so I would try to use BiocManager::install("XML"). Is there a single-word adjective for "having exceptionally strong moral principles"? March 1, 2023, 8:52pm DESeq2: Error: package or namespace load failed for 'DESeq2': objects Install DESeq2 through anaconda - Bioinformatics Stack Exchange 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. [R] Error: package or namespace load failed for 'ggplot2' in Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [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. 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 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.
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