[53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Learn more about Stack Overflow the company, and our products. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Press CTRL-C to abort. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. As such there are two solutions that may be more or less attainable given your own IT system. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. data . DESeq2_2301_76497647-CSDN Loading required package: GenomicRanges Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () rev2023.3.3.43278. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. .onLoad failed in loadNamespace() for 'rlang', details: [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 to your account. If you have a query related to it or one of the replies, start a new topic and refer back with a link. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Looking for incompatible packages. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Remember to always click on the red Show me the content on this page notice when navigating these older versions. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Is there a proper earth ground point in this switch box? nnet, spatial, survival. Why are physically impossible and logically impossible concepts considered separate in terms of probability? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? there is no package called Hmisc. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Please remember to confirm an answer once you've received one. Already on GitHub? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. I then launched the R application (from the finder, not RStudio) and installed BiocManager. + "htmlTable", "xfun" Warning: cannot remove prior installation of package xfun 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. Does anyone know why I'm getting the following message when I load tidyverse in a new session. It is working now. 1 RR. R https://www.jianshu.com/p/d9ca5a66cb72?v=1676346790161 2 ``` library (tidyverse) Error: package or namespace load failed for 'tidyverse' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'cli' 3.3.0>= 3.4.1 In addition: Warning message: Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Just realize that I need to write the script "library("DESeq2")" before I proceed. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Use this. In addition: Warning message: 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"). 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. Loading required package: GenomeInfoDb 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. library(DESeq2) I tried again and again was met with missing packages BUT!!! 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. Asking for help, clarification, or responding to other answers. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I've copied the output below in case it helps with troubleshooting. Any other suggestion? [5] IRanges_2.8.1 S4Vectors_0.12.1 The other option is to download and older version of locfit from the package archive and install manually. 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. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Well occasionally send you account related emails. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 2. Why is there a voltage on my HDMI and coaxial cables? One solution is to find all available packages. To learn more, see our tips on writing great answers. 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. [7] edgeR_3.16.5 limma_3.30.12 "After the incident", I started to be more careful not to trip over things. Also note, however, that the error you got has been associated in the past with mirror outages. No error messages are returned. 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: Policy. How can I fix error with loading package in R ? | ResearchGate By clicking Sign up for GitHub, you agree to our terms of service and "4.2") and enter: For older versions of R, please refer to the appropriate @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. [7] datasets methods base, other attached packages: [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 4. R DESeq2 - Making statements based on opinion; back them up with references or personal experience. Fortunately I was able to solve it by doing things from several suggested solutions. 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 am running a new install of R (3.5.0) and RStudio (1.1.414). Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Error when installing Aldex2 - Community Plugin Support - Open Source Acidity of alcohols and basicity of amines. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: So, supposedly the issue is with Hmisc. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. March 1, 2023, 3:25pm 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. 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 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Solving environment: Found conflicts! Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub What is the output of. 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 can download DESeq2 using, User Agreement and Privacy To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Use MathJax to format equations. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 [R] Error: package or namespace load failed for 'ggplot2' in Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc privacy statement. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. enter citation("DESeq2")): To install this package, start R (version Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. 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. How can we prove that the supernatural or paranormal doesn't exist? When an R package depends on a newer package version, the required package is downloaded but not loaded. I just figured Id ask. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? The package has place the R version constraint. "htmlTable", "xfun" Then I reinstalled R then Rstudio then RTools. ERROR: dependency Hmisc is not available for package DESeq2 if (!require("BiocManager", quietly = TRUE)) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Platform: x86_64-apple-darwin17.0 (64-bit) Installing Hmisc as suggested above did not solve the issue. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. R version 3.6.1 (2019-07-05) DESeq2 installation in R - Bioconductor 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. @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. installation of package GenomeInfoDbData had non-zero exit status. biocLite(), install.packages() (and the devtools equivalent?) [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 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 . ()library(DESeq2):Error in loadNamespace: no package called ""s When you load the package, you can observe this error. Just to add on -- do you require an old version of Bioconductor for your current project? Old packages: 'RcppArmadillo', 'survival' R version 4.0.1 (2020-06-06) Sounds like there might be an issue with conda setup? Try installing zip, and then loading olsrr. "After the incident", I started to be more careful not to trip over things. package xfun successfully unpacked and MD5 sums checked Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. library(caret) namespace load failed Object sigma not To subscribe to this RSS feed, copy and paste this URL into your RSS reader. - the incident has nothing to do with me; can I use this this way? If it fails, required operating system facilities are missing. Installing package(s) 'XML' Thank you @hharder. Give up and run everything from the "permitted" library location (e.g. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in 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. 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). This can take several minutes. 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"). So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin.