- the incident has nothing to do with me; can I use this this way? In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. 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. And finally, install the problem packages, perhaps also DESeq2. "4.2") and enter: For older versions of R, please refer to the appropriate Making statements based on opinion; back them up with references or personal experience. Old packages: 'RcppArmadillo', 'survival' Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) If you have a query related to it or one of the replies, start a new topic and refer back with a link. 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]]) : Also note, however, that the error you got has been associated in the past with mirror outages. DESeq2_2301_76497647-CSDN 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. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Find centralized, trusted content and collaborate around the technologies you use most. Installing package(s) 'GenomeInfoDbData' How do you ensure that a red herring doesn't violate Chekhov's gun? sessionInfo() To resolve this error, install the required package as a cluster-installed library. 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 think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. 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 guide. ()library(DESeq2):Error in loadNamespace: no package called ""s Why is this sentence from The Great Gatsby grammatical? I tried following the instructions for 2019.7 as well and I am getting the same error. Use this. I just figured Id ask. 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. Sign in How can we prove that the supernatural or paranormal doesn't exist? Already on GitHub? (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 . By clicking Sign up for GitHub, you agree to our terms of service and 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. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Running under: macOS Catalina 10.15.3, Matrix products: default Thanks for contributing an answer to Bioinformatics Stack Exchange! Running under: macOS Sierra 10.12.3, locale: 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. Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). 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. 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: The package has place the R version constraint. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE 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. This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 What am I doing wrong here in the PlotLegends specification? Rload failed - downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in 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. What is the output of. Not the answer you're looking for? install.packages("BiocManager"), I get this error: To learn more, see our tips on writing great answers. Do I need a thermal expansion tank if I already have a pressure tank? How do I align things in the following tabular environment? Erasmus+ funds available! [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. When you load the package, you can observe this error. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Thanks for contributing an answer to Stack Overflow! Policy. Content type 'application/zip' length 233860 bytes (228 KB) C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Is there anything I can do to speed it up? [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 How can I fix error with loading package in R ? | ResearchGate Follow Up: struct sockaddr storage initialization by network format-string. I'm having a similar error, but different package: library("DESeq2") library(DESeq2) 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 You are doing something very wrong when installing your packages. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Policy. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Have a question about this project? If it fails, required operating system facilities are missing. When an R package depends on a newer package version, the required package is downloaded but not loaded. March 1, 2023, 4:56pm If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I thought that working in a new environment would help, but it didnt. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. library(caret) namespace load failed Object sigma not Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Connect and share knowledge within a single location that is structured and easy to search. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Feedback Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 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"). Is there anyone the same as mine error while loading library(DESeq2)? 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): error: object 'rlang_dots_list' not found dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Let me confer with the team. 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 . Documentation I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Is a PhD visitor considered as a visiting scholar? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Bioconductor release. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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 /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Why do academics stay as adjuncts for years rather than move around? One solution is to find all available packages. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. This article explains how to resolve the package or namespace loading error. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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). Bioconductor - DESeq2 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. Sounds like you might have an issue with which R Rstudio is running. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 2. I guess that means we can finally close this issue. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Resolving package or namespace loading error .onLoad failed in loadNamespace() for 'rlang', details: Should I update the Bioconductor to latest version instead? [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Error: package or namespace load failed, object not found I also tried something I found on google: but the installation had errors too, I can write them here if needed. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Remember to always click on the red Show me the content on this page notice when navigating these older versions. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. I would recommend installing an older version of QIIME 2 for this plugin to work. Thank you @hharder. 9. MathJax reference. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Install DESeq2 through anaconda - Bioinformatics Stack Exchange ERROR: dependency Hmisc is not available for package DESeq2 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Warning message: How to use Slater Type Orbitals as a basis functions in matrix method correctly? Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Surly Straggler vs. other types of steel frames. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Just to add on -- do you require an old version of Bioconductor for your current project? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () sessionInfo() Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? This can take several minutes. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 No error messages are returned. If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. rev2023.3.3.43278. Update all/some/none? Then I reinstalled R then Rstudio then RTools. When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 If you try loading the DEseq2 library now, that might work. to your account. there is no package called Hmisc. 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. Connect and share knowledge within a single location that is structured and easy to search. 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. Are you sure the R you're running from the command line is installed through Anaconda as well? rev2023.3.3.43278. The other option is to download and older version of locfit from the package archive and install manually. 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 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Then I reinstalled R then Rstudio then RTools. Whats the grammar of "For those whose stories they are"? When you load the package, you can observe this error. 4. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Installing Hmisc as suggested above did not solve the issue. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. install.packages ("zip") Please try reinstalling rlang on a fresh session. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) in your system, start R and enter: Follow [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 After 3-4 manual installs everything worked. [R] Error: package or namespace load failed for 'ggplot2' in vegan) just to try it, does this inconvenience the caterers and staff? 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

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