[1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 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. Also make sure that you have RTools.exe installed and working. No error messages are returned. 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.
Install DESeq2 through anaconda - Bioinformatics Stack Exchange When you load the package, you can observe this error. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. install.packages('
', repo='http://nbcgib.uesc.br/mirrors/cran/'). I do know that it works well in qiime2-2020.6. and then updating the packages that command indicates. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Running under: macOS Catalina 10.15.3, Matrix products: default Surly Straggler vs. other types of steel frames. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Disconnect between goals and daily tasksIs it me, or the industry? Is there anyone the same as mine error while loading library(DESeq2)? Feedback to your account. Bad: conda install -c bioconda bioconductor-deseq2. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 2. Running. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Already on GitHub? Policy. 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: [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Remember to always click on the red Show me the content on this page notice when navigating these older versions. Just realize that I need to write the script "library("DESeq2")" before I proceed. package rlang was built under R version 3.5.1. To add to this, I have also been using DESeq2 recently and ran into the same problem. [R] Error: package or namespace load failed for 'ggplot2' in Join us at CRISPR workshops in Koper, Slovenia in 2023. DESeq2: Error: package or namespace load failed for 'DESeq2': objects sessionInfo() "4.2") and enter: For older versions of R, please refer to the appropriate I have tried your suggestion and also updating the packages that command indicates. 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"). So, supposedly the issue is with Hmisc. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) ()library(DESeq2):Error in loadNamespace: no package called ""s Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Not the answer you're looking for? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in R version 3.6.1 (2019-07-05) The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. From the console install.packages ("rlang") should fix this. Is there a proper earth ground point in this switch box? The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). DESeq2 - I can't get the library to load - Bioconductor Why are physically impossible and logically impossible concepts considered separate in terms of probability? [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Bioconductor release. nnet, spatial, survival. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Then I reinstalled R then Rstudio then RTools. Update all/some/none? Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. binary source needs_compilation Is there a single-word adjective for "having exceptionally strong moral principles"? enter citation("DESeq2")): To install this package, start R (version 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") Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Just to add on -- do you require an old version of Bioconductor for your current project? [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Thanks for contributing an answer to Stack Overflow! Making statements based on opinion; back them up with references or personal experience. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. 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. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' I am running a new install of R (3.5.0) and RStudio (1.1.414). May be the version has problem How can I do ? While a notebook is attached to a cluster, the R namespace cannot be refreshed. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 rev2023.3.3.43278. So if you still get this error try changing your CRAN mirror. 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"). Does anyone know why I'm getting the following message when I load tidyverse in a new session. 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. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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. Statistics ; Algorithm(ML, DL,.) Any suggestions would be greatly appreciated. Are there tables of wastage rates for different fruit and veg? Try again and choose No. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. How do I align things in the following tabular environment? C:\R\R-3.4.3\library). Sorry, I'm newbie. If not fixed, Try removing remove.packages (rlang) then. Installing package(s) 'XML' To subscribe to this RSS feed, copy and paste this URL into your RSS reader. installation of package GenomeInfoDbData had non-zero exit status. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat running multiple versions of the same package, keeping separate libraries for some projects). To learn more, see our tips on writing great answers. Loading required package: GenomeInfoDb I would like to install DESeq2 for DE analysis. there is no package called GenomeInfoDbData check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Sounds like you might have an issue with which R Rstudio is running. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': 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. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Follow Up: struct sockaddr storage initialization by network format-string. 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). I need help installing a package "DESeq2" having - RStudio Community Sign up for a free GitHub account to open an issue and contact its maintainers and the community. That plugin is has not been updated to work with later releases of QIIME 2. The package has place the R version constraint. 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!!! Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Find centralized, trusted content and collaborate around the technologies you use most. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages