Just to add on -- do you require an old version of Bioconductor for your current project? 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? Bad: conda install -c bioconda bioconductor-deseq2. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. In addition: Warning message: I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 2. Is there a proper earth ground point in this switch box? downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? MathJax reference. there is no package called locfit. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: nnet, spatial, survival. Why do academics stay as adjuncts for years rather than move around? 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. installation of package GenomeInfoDbData had non-zero exit status. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Language(R, Python, SQL) ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Please remember to confirm an answer once you've received one. So if you still get this error try changing your CRAN mirror. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' We've tried this - and can replicate this issue on a completely new install with no existing package installs. But I guess you have many problems with your installation, and I'd suggest. Connect and share knowledge within a single location that is structured and easy to search. 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. Is there a proper earth ground point in this switch box? Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. 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 tried again and again was met with missing packages BUT!!! Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide, You can try installing packages in R (which comes with R 3.5.1, not RStudio). [16] phyloseq1.30.0, loaded via a namespace (and not attached): Platform: x86_64-apple-darwin15.6.0 (64-bit) 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 . You are doing something very wrong when installing your packages. Policy. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. It only takes a minute to sign up. Policy. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) "4.2") and enter: For older versions of R, please refer to the appropriate install.packages("BiocManager"), I get this error: privacy statement. 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. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages 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. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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. How to use Slater Type Orbitals as a basis functions in matrix method correctly? in your system, start R and enter: Follow Fortunately I was able to solve it by doing things from several suggested solutions. + "htmlTable", "xfun" Policy. [69] tidyselect_1.0.0. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Try installing zip, and then loading olsrr. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I hope you can see something I can't see and help me solving this issue. How to notate a grace note at the start of a bar with lilypond? Running under: Windows 10 x64 (build 18362), locale: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Follow Up: struct sockaddr storage initialization by network format-string. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. To learn more, see our tips on writing great answers. In install.packages() : March 1, 2023, 7:31pm Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, 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 . [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Join us at CRISPR workshops in Koper, Slovenia in 2023. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 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 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 I can download DESeq2 using, User Agreement and Privacy Installing package(s) 'htmlTable', 'xfun' I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. 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). I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Why do academics stay as adjuncts for years rather than move around? @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. 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. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () 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'. Does a summoned creature play immediately after being summoned by a ready action? Sounds like you might have an issue with which R Rstudio is running. install.packages ("zip") "After the incident", I started to be more careful not to trip over things. If you try loading the DEseq2 library now, that might work. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. 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!!! Platform: x86_64-w64-mingw32/x64 (64-bit) Solution To resolve this error, install the required package as a cluster-installed library. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in That plugin is has not been updated to work with later releases of QIIME 2. 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 Documentation check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. 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. Please read the posting The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Have a question about this project? RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc package in your R session. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. It is working now. sessionInfo() + ), update = TRUE, ask = FALSE) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. [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. In file.copy(savedcopy, lib, recursive = TRUE) : Is there anything I can do to speed it up? 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]]): package rlang was built under R version 3.5.1. And finally, install the problem packages, perhaps also DESeq2. To add to this, I have also been using DESeq2 recently and ran into the same problem. Why do many companies reject expired SSL certificates as bugs in bug bounties?

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