I thought that working in a new environment would help, but it didnt. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Loading required package: GenomeInfoDb 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. I hope you can see something I can't see and help me solving this issue. You signed in with another tab or window. I do know that it works well in qiime2-2020.6. 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. Should I update the Bioconductor to latest version instead? Installation instructions to use this 1. Asking for help, clarification, or responding to other answers. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Already on GitHub? 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: I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. What is the output of. Not the answer you're looking for? there is no package called GenomeInfoDbData Thanks for contributing an answer to Stack Overflow! Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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]]) : - the incident has nothing to do with me; can I use this this way? [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: Making statements based on opinion; back them up with references or personal experience. so I would try to use BiocManager::install("XML"). When you load the package, you can observe this error. Why do academics stay as adjuncts for years rather than move around? nnet, spatial, survival Please try reinstalling rlang on a fresh session. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. it would be good to hear any speculation you have of how this might have happened). guide. If it fails, required operating system facilities are missing. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): :), BiocManager::install("locift") Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Loading required package: GenomicRanges When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. To view documentation for the version of this package installed 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. privacy statement. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 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. Is there anyone the same as mine error while loading library(DESeq2)? 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. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [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. Acidity of alcohols and basicity of amines. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. 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. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 running multiple versions of the same package, keeping separate libraries for some projects). This is the beauty of installing QIIME 2 via conda, you can have many different versions of QIIME 2 on your system at the same time and activate the version you want to use. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. While a notebook is attached to a cluster, the R namespace cannot be refreshed. 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. Installing package(s) 'htmlTable', 'xfun' Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Policy. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? 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. Just realize that I need to write the script "library("DESeq2")" before I proceed. Is there anything I can do to speed it up? Citation (from within R, How can we prove that the supernatural or paranormal doesn't exist? Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Does anyone know why I'm getting the following message when I load tidyverse in a new session. 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. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' there is no package called data.table R version 3.6.1 (2019-07-05) to allow custom library locations. It only takes a minute to sign up. 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 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Follow Up: struct sockaddr storage initialization by network format-string. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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 . [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 call: dots_list() BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Thanks for contributing an answer to Stack Overflow! [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . What do I need to do to reproduce your problem? 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'. When an R package depends on a newer package version, the required package is downloaded but not loaded. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Glad everything is finally working now. Fortunately I was able to solve it by doing things from several suggested solutions. Press CTRL-C to abort. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Sounds like there might be an issue with conda setup? I even tried BiocManager::install("XML") but all failed as shown below. To learn more, see our tips on writing great answers. What is a word for the arcane equivalent of a monastery? New replies are no longer allowed. [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: A place where magic is studied and practiced? there is no package called GenomeInfoDbData [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? May be the version has problem How can I do ? 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. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Also make sure that you have RTools.exe installed and working. + ), update = TRUE, ask = FALSE) How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages requires R 4 and running more than a couple of releases behind in R risks multiplying problems. enter citation("DESeq2")): To install this package, start R (version Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. . Warning: cannot remove prior installation of package xfun The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Solving environment: Found conflicts! Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 4. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Is there a proper earth ground point in this switch box? Content type 'application/zip' length 4255589 bytes (4.1 MB) Bad: conda install -c bioconda bioconductor-deseq2. sessionInfo() there is no package called Hmisc. library(caret) namespace load failed Object sigma not found caret , . [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [69] tidyselect_1.0.0. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). When you load the package, you can observe this error. if (!require("BiocManager", quietly = TRUE)) This can take several minutes. [7] datasets methods base, other attached packages: vegan) just to try it, does this inconvenience the caterers and staff? Thanks! The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 + "htmlTable", "xfun" To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR @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. I would like to install DESeq2 for DE analysis. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Use MathJax to format equations. Use of this site constitutes acceptance of our User Agreement and Privacy I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. Have a question about this project? This includes any installed libraries. - the incident has nothing to do with me; can I use this this way? I've copied the output below in case it helps with troubleshooting. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Platform: x86_64-apple-darwin13.4.0 (64-bit) Did you do that? How to use Slater Type Orbitals as a basis functions in matrix method correctly? I'm trying to reproduce your problem, so being as precise as possible is important. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Whats the grammar of "For those whose stories they are"? More info about Internet Explorer and Microsoft Edge. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Please read the posting 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. Running under: macOS Sierra 10.12.3, locale: What am I doing wrong here in the PlotLegends specification? install.packages('
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