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. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? to your account. 4. Rload failed - 9. enter citation("DESeq2")): To install this package, start R (version Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Is there anyone the same as mine error while loading library(DESeq2)? binary source needs_compilation Looking for incompatible packages. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. The package has place the R version constraint. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Post questions about Bioconductor Platform: x86_64-apple-darwin13.4.0 (64-bit) [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) there is no package called GenomeInfoDbData Find centralized, trusted content and collaborate around the technologies you use most. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Platform: x86_64-apple-darwin15.6.0 (64-bit) Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) 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!!! [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [5] IRanges_2.8.1 S4Vectors_0.12.1 there is no package called Hmisc. 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. Sign in Traffic: 307 users visited in the last hour, I am new to all this! package xfun successfully unpacked and MD5 sums checked One solution is to find all available packages. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 [7] edgeR_3.16.5 limma_3.30.12 Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). call: dots_list() Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Policy. Is there a proper earth ground point in this switch box? 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. Have you tried install.packages("locfit") ? 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. Just updated my previous R to 4.01 and now I cant load DESeq2. Why do academics stay as adjuncts for years rather than move around? [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 + "htmlTable", "xfun" Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Please remember to confirm an answer once you've received one. MathJax reference. 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. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Is a PhD visitor considered as a visiting scholar? I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Just realize that I need to write the script "library("DESeq2")" before I proceed. Any other suggestion? 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. To learn more, see our tips on writing great answers. Use of this site constitutes acceptance of our User Agreement and Privacy What do I need to do to reproduce your problem? Looking for incompatible packages.This can take several minutes. 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: Thanks for contributing an answer to Stack Overflow! [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Error: package or namespace load failed, object not found Citation (from within R, By clicking Sign up for GitHub, you agree to our terms of service and The best answers are voted up and rise to the top, Not the answer you're looking for? I'm having a similar error, but different package: library("DESeq2") DESeq2_2301_76497647-CSDN C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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). That plugin is has not been updated to work with later releases of QIIME 2. I hope you can see something I can't see and help me solving this issue. ()library(DESeq2):Error in loadNamespace: no package called ""s By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I can download DESeq2 using, User Agreement and Privacy Use this. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. More info about Internet Explorer and Microsoft Edge. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Start R to confirm they are gone. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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. This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. Convince your IT department to relax the permissions for R packages To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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 am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. New replies are no longer allowed. To learn more, see our tips on writing great answers. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Installing package(s) 'htmlTable', 'xfun' From the console install.packages ("rlang") should fix this. I am running a new install of R (3.5.0) and RStudio (1.1.414). Content type 'application/zip' length 386703 bytes (377 KB) package in your R session. To add to this, I have also been using DESeq2 recently and ran into the same problem. Is there a single-word adjective for "having exceptionally strong moral principles"? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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). LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. 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. How do you ensure that a red herring doesn't violate Chekhov's gun? 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: May be the version has problem How can I do ? Not the answer you're looking for? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: library(caret) namespace load failed Object sigma not found caret , . Content type 'application/zip' length 233860 bytes (228 KB) ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, While a notebook is attached to a cluster, the R namespace cannot be refreshed. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 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. :), BiocManager::install("locift") Give up and run everything from the "permitted" library location (e.g. May I know is there any other approach I can try? Styling contours by colour and by line thickness in QGIS. How to use Slater Type Orbitals as a basis functions in matrix method correctly? package rlang was built under R version 3.5.1. there is no package called data.table 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. Is there a proper earth ground point in this switch box? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Statistics ; Algorithm(ML, DL,.) Use MathJax to format equations. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 C:\R\R-3.4.3\library). .onLoad failed in loadNamespace() for 'rlang', details: [a/s/n]: 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 includes any installed libraries. 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"). Connect and share knowledge within a single location that is structured and easy to search. Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. I installed the package successfully with conda, but Rstudio is apparently does not know about it. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Already on GitHub? R version 3.6.1 (2019-07-05) Join us at CRISPR workshops in Koper, Slovenia in 2023. nnet, spatial, survival [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Connect and share knowledge within a single location that is structured and easy to search. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Then I reinstalled R then Rstudio then RTools. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. - the incident has nothing to do with me; can I use this this way? Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Error when installing Aldex2 - Community Plugin Support - Open Source Thanks for contributing an answer to Bioinformatics Stack Exchange! A place where magic is studied and practiced? I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Install DESeq2 through anaconda - Bioinformatics Stack Exchange 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"). You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) It is working now. install.packages ("zip") I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. I tried to download the "locfit" package but I can't find it anywhere. How to notate a grace note at the start of a bar with lilypond? in your system, start R and enter: Follow 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'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. Does a summoned creature play immediately after being summoned by a ready action? 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 But I guess you have many problems with your installation, and I'd suggest. (Factorization). Follow Up: struct sockaddr storage initialization by network format-string. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Warning message: [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 library(DESeq2) 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. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Choose Yes. Is there anything I can do to speed it 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 Well occasionally send you account related emails. Running. "After the incident", I started to be more careful not to trip over things. As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. Resolving package or namespace loading error
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