error: package or namespace load failed for 'deseq2

[25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 What is the output of. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 4. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so a, There are binary versions available but the source versions are later: The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Find centralized, trusted content and collaborate around the technologies you use most. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. Already on GitHub? When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. 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 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 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. Running under: Windows 10 x64 (build 18362), locale: Loading required package: GenomicRanges Platform: x86_64-w64-mingw32/x64 (64-bit) What am I doing wrong here in the PlotLegends specification? 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. Use of this site constitutes acceptance of our User Agreement and Privacy What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Why do academics stay as adjuncts for years rather than move around? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. What is a word for the arcane equivalent of a monastery? 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. Content type 'application/zip' length 386703 bytes (377 KB) 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. I would like to install DESeq2 for DE analysis. 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). To learn more, see our tips on writing great answers. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Why do many companies reject expired SSL certificates as bugs in bug bounties? [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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. How do you ensure that a red herring doesn't violate Chekhov's gun? Please try the following steps: Quit all R/Rstudio sessions. Asking for help, clarification, or responding to other answers. there is no package called Hmisc. Running under: macOS Sierra 10.12.6. [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. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Retrying with flexible solve.Solving environment: Found conflicts! May I know is there any other approach I can try? 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? Running under: macOS Catalina 10.15.3, Matrix products: default If not fixed, Try removing remove.packages (rlang) then. 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 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Policy. Try installing zip, and then loading olsrr. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Give up and run everything from the "permitted" library location (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. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. A place where magic is studied and practiced? sessionInfo() [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( privacy statement. and then updating the packages that command indicates. 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"). Sounds like you might have an issue with which R Rstudio is running. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 I hope you can see something I can't see and help me solving this issue. Then I reinstalled R then Rstudio then RTools. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc 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 Learn more about Stack Overflow the company, and our products. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Running. When an R package depends on a newer package version, the required package is downloaded but not loaded. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. I was assuming that to be the case. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Traffic: 307 users visited in the last hour, I am new to all this! [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Sounds like there might be an issue with conda setup? ERROR: lazy loading failed for package Hmisc This topic was automatically closed 21 days after the last reply. Does anyone know why I'm getting the following message when I load tidyverse in a new session. What do I need to do to reproduce your problem? I've copied the output below in case it helps with troubleshooting. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). @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. To view documentation for the version of this package installed I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Use MathJax to format equations. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. binary source needs_compilation @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. If it fails, required operating system facilities are missing. I highly recommend that any R/RStudio version not installed inside conda be removed. Installing package(s) 'XML' Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Asking for help, clarification, or responding to other answers. The best answers are voted up and rise to the top, Not the answer you're looking for? Not the answer you're looking for? So if you still get this error try changing your CRAN mirror. Glad everything is finally working now. Replacing broken pins/legs on a DIP IC package. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Thanks for contributing an answer to Stack Overflow! 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. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). I am running a new install of R (3.5.0) and RStudio (1.1.414). I even tried BiocManager::install("XML") but all failed as shown below. Installing Hmisc as suggested above did not solve the issue. I tried following the instructions for 2019.7 as well and I am getting the same error. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? call: dots_list() The package has place the R version constraint. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. (Factorization). 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. Warning message: 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. 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: You are doing something very wrong when installing your packages. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? How can we prove that the supernatural or paranormal doesn't exist? I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. running multiple versions of the same package, keeping separate libraries for some projects). If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Whats the grammar of "For those whose stories they are"? there is no package called GenomeInfoDbData Let me confer with the team. + ), update = TRUE, ask = FALSE) Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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 While a notebook is attached to a cluster, the R namespace cannot be refreshed. 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. rev2023.3.3.43278. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Platform: x86_64-apple-darwin13.4.0 (64-bit) New replies are no longer allowed. 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. So, supposedly the issue is with Hmisc. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. I'm having a similar error, but different package: library("DESeq2") Are you sure the R you're running from the command line is installed through Anaconda as well? 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.

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