[7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Install DESeq2 through anaconda - Bioinformatics Stack Exchange Making statements based on opinion; back them up with references or personal experience. Policy. data . I have tried your suggestion and also updating the packages that command indicates. - the incident has nothing to do with me; can I use this this way? [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 I can download DESeq2 using, User Agreement and Privacy Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Any suggestions would be greatly appreciated. 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. nnet, spatial, survival - the incident has nothing to do with me; can I use this this way? More info about Internet Explorer and Microsoft Edge. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I then launched the R application (from the finder, not RStudio) and installed BiocManager. R version 3.6.1 (2019-07-05) to your account. Bad: conda install -c bioconda bioconductor-deseq2. Any other suggestion? Disconnect between goals and daily tasksIs it me, or the industry? When you load the package, you can observe this error. [5] IRanges_2.8.1 S4Vectors_0.12.1 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. 1. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. I'm having a similar error, but different package: library("DESeq2") Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Finally After 3-4 manual installations of missing packages everything worked. install.packages("BiocManager"), I get this error: downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked If you have a query related to it or one of the replies, start a new topic and refer back with a link. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Installing package(s) 'GenomeInfoDbData' there is no package called GenomeInfoDbData A place where magic is studied and practiced? If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Is the God of a monotheism necessarily omnipotent? However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. After 3-4 manual installs everything worked. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 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. 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. If you try loading the DEseq2 library now, that might work. Is a PhD visitor considered as a visiting scholar? When an R package depends on a newer package version, the required package is downloaded but not loaded. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. So, supposedly the issue is with Hmisc. 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 . Why is this sentence from The Great Gatsby grammatical? Open Source Biology & Genetics Interest Group. 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: library(caret) namespace load failed Object sigma not :), BiocManager::install("locift") 9. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 I would recommend installing an older version of QIIME 2 for this plugin to work. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? This topic was automatically closed 21 days after the last reply. 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]]): + ), update = TRUE, ask = FALSE) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Have a question about this project? LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: privacy statement. Rload failed - I would like to install DESeq2 for DE analysis. Follow Up: struct sockaddr storage initialization by network format-string. [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: March 1, 2023, 7:31pm sessionInfo() + "htmlTable", "xfun" Try installing zip, and then loading olsrr. 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. 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. there is no package called data.table While a notebook is attached to a cluster, the R namespace cannot be refreshed. Is there a proper earth ground point in this switch box? If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : MathJax reference. Find centralized, trusted content and collaborate around the technologies you use most. I've copied the output below in case it helps with troubleshooting. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I highly recommend that any R/RStudio version not installed inside conda be removed. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Policy. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. 4. If not fixed, Try removing remove.packages (rlang) then. 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 to allow custom library locations. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Convince your IT department to relax the permissions for R packages 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. error: object 'rlang_dots_list' not found Use MathJax to format equations. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Sorry, I'm newbie. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Policy. "After the incident", I started to be more careful not to trip over things. Is there anything I can do to speed it up? The other option is to download and older version of locfit from the package archive and install manually. No error messages are returned. 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. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. One solution is to find all available packages. it would be good to hear any speculation you have of how this might have happened). 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 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. a, There are binary versions available but the source versions are later: To learn more, see our tips on writing great answers. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: So if you still get this error try changing your CRAN mirror. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 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 . Please remember to confirm an answer once you've received one. Use of this site constitutes acceptance of our User Agreement and Privacy March 1, 2023, 8:52pm Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Let me confer with the team. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Platform: x86_64-w64-mingw32/x64 (64-bit) Platform: x86_64-apple-darwin15.6.0 (64-bit) [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Is there a single-word adjective for "having exceptionally strong moral principles"? Installation instructions to use this Hello, BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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. I tried following the instructions for 2019.7 as well and I am getting the same error. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: DESeq2 installation in R - Bioconductor By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. How can we prove that the supernatural or paranormal doesn't exist? [13] ggplot23.3.0 car3.0-7 carData3.0-3 Content type 'application/zip' length 386703 bytes (377 KB) Running under: Windows 10 x64 (build 18362), locale: biocLite(), install.packages() (and the devtools equivalent?) The package has place the R version constraint. You signed in with another tab or window. [a/s/n]: I guess that means we can finally close this issue. Running. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Warning: restored xfun, The downloaded binary packages are in Feedback 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. [16] phyloseq1.30.0, loaded via a namespace (and not attached): Do I need a thermal expansion tank if I already have a pressure tank? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). The error states that the current version is 0.4.5 but 0.4.10 is required. How do I align things in the following tabular environment? ()library(DESeq2):Error in loadNamespace: no package called ""s im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. I thought that working in a new environment would help, but it didnt. binary source needs_compilation "4.2") and enter: For older versions of R, please refer to the appropriate Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Traffic: 307 users visited in the last hour, I am new to all this! My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Use of this site constitutes acceptance of our User Agreement and Privacy The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. March 1, 2023, 4:56pm Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Policy. and then updating the packages that command indicates. I tried to download the "locfit" package but I can't find it anywhere. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in This includes any installed libraries. May be the version has problem How can I do ? Just realize that I need to write the script "library("DESeq2")" before I proceed. I tried again and again was met with missing packages BUT!!! "htmlTable", "xfun" [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 I just figured Id ask. 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 Learn more about Stack Overflow the company, and our products. Please try the following steps: Quit all R/Rstudio sessions. 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. 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").
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