[9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Solving environment: Found conflicts! 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. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Join us at CRISPR workshops in Koper, Slovenia in 2023. 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 R version 3.6.1 (2019-07-05) I highly recommend that any R/RStudio version not installed inside conda be removed. I also tried something I found on google: but the installation had errors too, I can write them here if needed. I even tried BiocManager::install("XML") but all failed as shown below. 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. rev2023.3.3.43278. May I know is there any other approach I can try? Installing Hmisc as suggested above did not solve the issue. 4. In addition: Warning message: there is no package called GenomeInfoDbData [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 I tried again and again was met with missing packages BUT!!! By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Disconnect between goals and daily tasksIs it me, or the industry? Also note, however, that the error you got has been associated in the past with mirror outages. Are you sure the R you're running from the command line is installed through Anaconda as well?
[29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? library(DESeq2) 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). [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: Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. a, There are binary versions available but the source versions are later: Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. 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"). (Factorization). Installing package(s) 'GenomeInfoDbData' to your account. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Finally After 3-4 manual installations of missing packages everything worked.
After 3-4 manual installs everything worked. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 You are doing something very wrong when installing your packages. install.packages ("zip") downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Running. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Now loading the DESeq2 library (Errors): Because I already installed >10 packages by hand I assume the solution is not to keep installing the missing packages because those packages will have more missing packages and more and more and I won't get out of this loop. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. @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. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Surly Straggler vs. other types of steel frames. 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]]): I guess that means we can finally close this issue. March 1, 2023, 7:31pm Please remember to confirm an answer once you've received one. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Post questions about Bioconductor When you load the package, you can observe this error. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. 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.
()library(DESeq2):Error in loadNamespace: no package called ""s Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so The best answers are voted up and rise to the top, Not the answer you're looking for? Is there a single-word adjective for "having exceptionally strong moral principles"? data . Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I am running a new install of R (3.5.0) and RStudio (1.1.414). Platform: x86_64-apple-darwin13.4.0 (64-bit) rev2023.3.3.43278. library(caret) namespace load failed Object sigma not found caret , . /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. - the incident has nothing to do with me; can I use this this way? Is there a proper earth ground point in this switch box?
Bioconductor - DESeq2 downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [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 trying to reproduce your problem, so being as precise as possible is important. R version 3.6.3 (2020-02-29) so I would try to use BiocManager::install("XML"). Thanks for contributing an answer to Stack Overflow! Thank you @hharder. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Please try reinstalling rlang on a fresh session. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? How can we prove that the supernatural or paranormal doesn't exist? Running under: Windows 10 x64 (build 18362), locale: Feedback Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0
R DESeq2 - Have you tried install.packages("locfit") ? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? . Warning: restored xfun, The downloaded binary packages are in - the incident has nothing to do with me; can I use this this way?
I need help installing a package "DESeq2" having - RStudio Community Documentation [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 What am I doing wrong here in the PlotLegends specification?
Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Styling contours by colour and by line thickness in QGIS. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Why do academics stay as adjuncts for years rather than move around? 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. ERROR: dependency Hmisc is not available for package DESeq2 Open Source Biology & Genetics Interest Group. You signed in with another tab or window. To learn more, see our tips on writing great answers. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) The package has place the R version constraint. What is the output of. 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]]) : Language(R, Python, SQL) Is a PhD visitor considered as a visiting scholar? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Looking for incompatible packages. Update all/some/none? Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. More info about Internet Explorer and Microsoft Edge. "After the incident", I started to be more careful not to trip over things. 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. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? So, supposedly the issue is with Hmisc. The other option is to download and older version of locfit from the package archive and install manually. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) We've tried this - and can replicate this issue on a completely new install with no existing package installs. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 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. 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. Please try the following steps: Quit all R/Rstudio sessions. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 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. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5
[R] Error: package or namespace load failed for 'ggplot2' in nnet, spatial, survival. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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. Why is this sentence from The Great Gatsby grammatical? But I guess you have many problems with your installation, and I'd suggest BiocManager::valid ()
DESeq2: Error: package or namespace load failed for 'DESeq2': objects If it fails, required operating system facilities are missing. 9. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. there is no package called GenomeInfoDbData I've copied the output below in case it helps with troubleshooting. By clicking Sign up for GitHub, you agree to our terms of service and It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 running multiple versions of the same package, keeping separate libraries for some projects). This includes any installed libraries. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: 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 . When an R package depends on a newer package version, the required package is downloaded but not loaded. Installation instructions to use this 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 You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. [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: 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. It is working now. I do know that it works well in qiime2-2020.6. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Asking for help, clarification, or responding to other answers. Content type 'application/zip' length 386703 bytes (377 KB) Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. If you preorder a special airline meal (e.g. When you load the package, you can observe this error. Are there tables of wastage rates for different fruit and veg? A place where magic is studied and practiced? Remember to always click on the red Show me the content on this page notice when navigating these older versions. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. In file.copy(savedcopy, lib, recursive = TRUE) : 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. "htmlTable", "xfun" binary source needs_compilation Surly Straggler vs. other types of steel frames. Policy. That plugin is has not been updated to work with later releases of QIIME 2. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Running under: macOS Catalina 10.15.3, Matrix products: default Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers.
DESeq2 - I can't get the library to load - Bioconductor 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. Please read the posting Follow Up: struct sockaddr storage initialization by network format-string. I would recommend installing an older version of QIIME 2 for this plugin to work. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Loading required package: GenomicRanges Then I reinstalled R then Rstudio then RTools. 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. install.packages('
', repo='http://nbcgib.uesc.br/mirrors/cran/'). I tried to download the "locfit" package but I can't find it anywhere. This can take several minutes. Use this. [7] datasets methods base, other attached packages: guide. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Platform: x86_64-apple-darwin15.6.0 (64-bit) it would be good to hear any speculation you have of how this might have happened). there is no package called data.table Give up and run everything from the "permitted" library location (e.g. Have a question about this project? 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. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Choose Yes. 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 . Replacing broken pins/legs on a DIP IC package. I then launched the R application (from the finder, not RStudio) and installed BiocManager. rev2023.3.3.43278. Installing package(s) 'htmlTable', 'xfun' [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Glad everything is finally working now. 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 You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Whats the grammar of "For those whose stories they are"? [13] ggplot23.3.0 car3.0-7 carData3.0-3 How to use Slater Type Orbitals as a basis functions in matrix method correctly? Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. R| - Any other suggestion? [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 "After the incident", I started to be more careful not to trip over things. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Is there a proper earth ground point in this switch box? Sorry, I'm newbie. Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or? Does anyone know why I'm getting the following message when I load tidyverse in a new session. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? package rlang was built under R version 3.5.1. Warning message: installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat 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. New replies are no longer allowed. 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"). Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) 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: I was assuming that to be the case. Sign in Warning message: [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 I'm having a similar error, but different package: library("DESeq2") Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 package xfun successfully unpacked and MD5 sums checked Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. Making statements based on opinion; back them up with references or personal experience. 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. library(DESeq2) 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. In install.packages() : Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Solution To resolve this error, install the required package as a cluster-installed library. Use MathJax to format equations. Try again and choose No. Does a summoned creature play immediately after being summoned by a ready action? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Use of this site constitutes acceptance of our User Agreement and Privacy How do I align things in the following tabular environment? Learn more about Stack Overflow the company, and our products. How can I fix error with loading package in R ? | ResearchGate there is no package called locfit. 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. This article explains how to resolve the package or namespace loading error. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Policy. Just realize that I need to write the script "library("DESeq2")" before I proceed. :), BiocManager::install("locift") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Loading required package: GenomeInfoDb [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Also make sure that you have RTools.exe installed and working. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': installation of package GenomeInfoDbData had non-zero exit status. 2. Then I reinstalled R then Rstudio then RTools. 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.
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