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If not fixed, Try removing remove.packages (rlang) then. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in now when I tried installing the missing packages they did install. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 9. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. New replies are no longer allowed. Sorry, I'm newbie. Sounds like there might be an issue with conda setup? Is a PhD visitor considered as a visiting scholar? 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 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. and then updating the packages that command indicates. to allow custom library locations. Follow Up: struct sockaddr storage initialization by network format-string. Whats the grammar of "For those whose stories they are"? What am I doing wrong here in the PlotLegends specification? Content type 'application/zip' length 386703 bytes (377 KB) [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Feedback
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. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. What is a word for the arcane equivalent of a monastery? Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Sounds like you might have an issue with which R Rstudio is running. "After the incident", I started to be more careful not to trip over things. I have tried your suggestion and also updating the packages that command indicates. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 I also tried something I found on google: but the installation had errors too, I can write them here if needed. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): So, supposedly the issue is with Hmisc. When you load the package, you can observe this error. By clicking Sign up for GitHub, you agree to our terms of service and Running under: macOS Catalina 10.15.3, Matrix products: default This article explains how to resolve the package or namespace loading error. @Tung I've updated my R and RStudio versions (unfortunately I had to first convince my workplace to approve them) and installed the packages through R 3.5.1 however, I'm still getting the same rlang error. Solving environment: Found conflicts! Have you tried install.packages("locfit") ? installation of package GenomeInfoDbData had non-zero exit status. 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. Asking for help, clarification, or responding to other answers. Installing package(s) 'GenomeInfoDbData' 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. We've tried this - and can replicate this issue on a completely new install with no existing package installs. 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. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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. First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). 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. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 1. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Installing package(s) 'XML'
DESeq2: Error: package or namespace load failed for 'DESeq2': objects there is no package called data.table to your account. Running. Use this. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. enter citation("DESeq2")): To install this package, start R (version (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 . May be the version has problem How can I do ? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. install.packages ("zip") 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, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy Just updated my previous R to 4.01 and now I cant load DESeq2. Running under: macOS Sierra 10.12.6. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 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'. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. How do you ensure that a red herring doesn't violate Chekhov's gun? there is no package called Hmisc. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [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. 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. Making statements based on opinion; back them up with references or personal experience. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. I am running a new install of R (3.5.0) and RStudio (1.1.414). Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Bad: conda install -c bioconda bioconductor-deseq2. Find centralized, trusted content and collaborate around the technologies you use most. Give up and run everything from the "permitted" library location (e.g.
R| - R version 3.6.3 (2020-02-29) Try installing zip, and then loading olsrr. If you have a query related to it or one of the replies, start a new topic and refer back with a link. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Connect and share knowledge within a single location that is structured and easy to search. Asking for help, clarification, or responding to other answers. To learn more, see our tips on writing great answers. package rlang was built under R version 3.5.1. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 To view documentation for the version of this package installed I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Solution To resolve this error, install the required package as a cluster-installed library. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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. Any other suggestion? [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4
DESeq2_2301_76497647-CSDN dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 2. it would be good to hear any speculation you have of how this might have happened). . Styling contours by colour and by line thickness in QGIS. If you preorder a special airline meal (e.g. 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. Connect and share knowledge within a single location that is structured and easy to search. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Sorry if I missed this, the question was quite long so I kind of skimmed, but I noticed that early on some of the packages were reported as requiring manual compilation from source. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 (Factorization). Use of this site constitutes acceptance of our User Agreement and Privacy Any suggestions would be greatly appreciated. ERROR: lazy loading failed for package Hmisc package xfun successfully unpacked and MD5 sums checked library(DESeq2) "After the incident", I started to be more careful not to trip over things.
How to use Slater Type Orbitals as a basis functions in matrix method correctly? .onLoad failed in loadNamespace() for 'rlang', details: By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy.
[R] Error: package or namespace load failed for 'ggplot2' in I was assuming that to be the case. If I run install.packages(GenomeInfoDb) from R console, it is telling me that the package is not available for R version 3.5.1. 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. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. The best answers are voted up and rise to the top, Not the answer you're looking for? 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 Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 After 3-4 manual installs everything worked. To add to this, I have also been using DESeq2 recently and ran into the same problem. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Remember to always click on the red Show me the content on this page notice when navigating these older versions. Surly Straggler vs. other types of steel frames. Should I update the Bioconductor to latest version instead? im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. [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: The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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. - the incident has nothing to do with me; can I use this this way? Hello, Is there anyone the same as mine error while loading library(DESeq2)? in your system, start R and enter: Follow Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Acidity of alcohols and basicity of amines. Looking for incompatible packages. Please try the following steps: Quit all R/Rstudio sessions. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Why do academics stay as adjuncts for years rather than move around? there is no package called locfit. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Finally After 3-4 manual installations of missing packages everything worked.
May I know is there any other approach I can try? Why do academics stay as adjuncts for years rather than move around? Convince your IT department to relax the permissions for R packages Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, 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!!! To learn more, see our tips on writing great answers. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 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. As such there are two solutions that may be more or less attainable given your own IT system. Please try reinstalling rlang on a fresh session. Old packages: 'RcppArmadillo', 'survival' 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") I guess that means we can finally close this issue. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Not the answer you're looking for? How do I align things in the following tabular environment? Warning: cannot remove prior installation of package xfun The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Warning: restored xfun, The downloaded binary packages are in Not the answer you're looking for? library(caret) namespace load failed Object sigma not found caret , .
Install DESeq2 through anaconda - Bioinformatics Stack Exchange unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 call: dots_list() [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: if (!require("BiocManager", quietly = TRUE)) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 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: