error: package or namespace load failed for 'deseq2

9. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 nnet, spatial, survival. [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: [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [69] tidyselect_1.0.0. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Is there a proper earth ground point in this switch box? sessionInfo() Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib (Factorization). guide. Give up and run everything from the "permitted" library location (e.g. [7] datasets methods base, other attached packages: there is no package called locfit. I highly recommend that any R/RStudio version not installed inside conda be removed. Try installing zip, and then loading olsrr. Error: package or namespace load failed for 'DESeq2 - Bioconductor 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 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. ()library(DESeq2):Error in loadNamespace: no package called ""s March 1, 2023, 3:25pm it would be good to hear any speculation you have of how this might have happened). 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. sessionInfo() BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [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. - the incident has nothing to do with me; can I use this this way? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? package rlang was built under R version 3.5.1. install.packages("BiocManager"), I get this error: [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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 [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 DESeq2 - I can't get the library to load - Bioconductor Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): March 1, 2023, 4:56pm rev2023.3.3.43278. I need help installing a package "DESeq2" having - RStudio Community Then I reinstalled R then Rstudio then RTools. Can't Load R DESeq2 Library, Installed All Missing Packages and Still It only takes a minute to sign up. May be the version has problem How can I do ? Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. @artembus Sounds like it was a ton of work! there is no package called GenomeInfoDbData It is working now. How to use Slater Type Orbitals as a basis functions in matrix method correctly? I tried again and again was met with missing packages BUT!!! By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Open Source Biology & Genetics Interest Group. Thanks for your suggestion. Connect and share knowledge within a single location that is structured and easy to search. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. so I would try to use BiocManager::install("XML"). It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 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. March 1, 2023, 7:31pm dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Looking for incompatible packages. Use of this site constitutes acceptance of our User Agreement and Privacy Policy. 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!!! Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). 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. Why do academics stay as adjuncts for years rather than move around? unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Content type 'application/zip' length 4255589 bytes (4.1 MB) Content type 'application/zip' length 233860 bytes (228 KB) Is there anything I can do to speed it up? [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): "htmlTable", "xfun" How can I fix error with loading package in R ? | ResearchGate Any suggestions would be greatly appreciated. In addition: Warning message: Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Whats the grammar of "For those whose stories they are"? I tried following the instructions for 2019.7 as well and I am getting the same error. [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Please read the posting now when I tried installing the missing packages they did install. 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. 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. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Have a question about this project? Just realize that I need to write the script "library("DESeq2")" before I proceed. 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. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 install.packages ("zip") How can we prove that the supernatural or paranormal doesn't exist? Error: package or namespace load failed, object not found C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages You are doing something very wrong when installing your packages. 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 Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. Asking for help, clarification, or responding to other answers. call: dots_list() rstudio - Error: package or namespace load failed for 'tidyverse [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. More info about Internet Explorer and Microsoft Edge. Replacing broken pins/legs on a DIP IC package. 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 To resolve this error, install the required package as a cluster-installed library. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. I was assuming that to be the case. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) library(caret) namespace load failed Object sigma not Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) The error states that the current version is 0.4.5 but 0.4.10 is required. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Looking for incompatible packages.This can take several minutes. And finally, install the problem packages, perhaps also DESeq2. I tried to download the "locfit" package but I can't find it anywhere. Feedback One solution is to find all available packages. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. 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. Please remember to confirm an answer once you've received one. 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: 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. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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 DESeq2 installation in R - Bioconductor Installing package(s) 'htmlTable', 'xfun' RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Remember to always click on the red Show me the content on this page notice when navigating these older versions. to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip'

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