Whats the grammar of "For those whose stories they are"? enter citation("DESeq2")): To install this package, start R (version Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Installing Hmisc as suggested above did not solve the issue. From the console install.packages ("rlang") should fix this. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 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. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. there is no package called GenomeInfoDbData /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages nnet, spatial, survival. Why do many companies reject expired SSL certificates as bugs in bug bounties? R version 3.6.1 (2019-07-05) Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Error: package GenomeInfoDb could not be loaded. [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. Content type 'application/zip' length 4255589 bytes (4.1 MB) Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 How do you ensure that a red herring doesn't violate Chekhov's gun? As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: . [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Connect and share knowledge within a single location that is structured and easy to search. library(caret) namespace load failed Object sigma not found caret , . C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: I'm having a similar error, but different package: library("DESeq2") The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? I've copied the output below in case it helps with troubleshooting. Is the God of a monotheism necessarily omnipotent? 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. How do I align things in the following tabular environment? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Learn more about Stack Overflow the company, and our products. Thank you @hharder. In install.packages() : 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. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under 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'. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? I am running a new install of R (3.5.0) and RStudio (1.1.414). [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Platform: x86_64-apple-darwin17.0 (64-bit) install.packages ("zip") install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Replacing broken pins/legs on a DIP IC package. Open Source Biology & Genetics Interest Group. If it fails, required operating system facilities are missing. I was assuming that to be the case. I would recommend installing an older version of QIIME 2 for this plugin to work. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 1. 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-apple-darwin15.6.0 (64-bit) Warning message: Citation (from within R, Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Are there tables of wastage rates for different fruit and veg? R version 4.0.1 (2020-06-06) When you load the package, you can observe this error. 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. Please read the posting Looking for incompatible packages.This can take several minutes. A place where magic is studied and practiced? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) binary source needs_compilation Thanks for contributing an answer to Bioinformatics Stack Exchange! Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 After 3-4 manual installs everything worked. Whats the grammar of "For those whose stories they are"? 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. data . requires R 4 and running more than a couple of releases behind in R risks multiplying problems. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. By clicking Sign up for GitHub, you agree to our terms of service and How to use Slater Type Orbitals as a basis functions in matrix method correctly? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in So, supposedly the issue is with Hmisc. 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. You signed in with another tab or window. Running under: macOS Sierra 10.12.3, locale: Is a PhD visitor considered as a visiting scholar? Not the answer you're looking for? so I would try to use BiocManager::install("XML"). 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. - the incident has nothing to do with me; can I use this this way? 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 are physically impossible and logically impossible concepts considered separate in terms of probability? [69] tidyselect_1.0.0. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. [1] stats4 parallel stats graphics grDevices utils This article explains how to resolve the package or namespace loading error. I hope you can see something I can't see and help me solving this issue. Thanks for contributing an answer to Stack Overflow! [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Bad: conda install -c bioconda bioconductor-deseq2. if (!require("BiocManager", quietly = TRUE)) Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. So if you still get this error try changing your CRAN mirror. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. and then updating the packages that command indicates. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' How can we prove that the supernatural or paranormal doesn't exist? package xfun successfully unpacked and MD5 sums checked [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Try again and choose No. sessionInfo() [a/s/n]: [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 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. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Hello, What do I need to do to reproduce your problem? 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. package in your R session. Then I reinstalled R then Rstudio then RTools. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. We've tried this - and can replicate this issue on a completely new install with no existing package installs. If you preorder a special airline meal (e.g. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Use of this site constitutes acceptance of our User Agreement and Privacy 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. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 I tried following the instructions for 2019.7 as well and I am getting the same error. No error messages are returned. ERROR: dependency Hmisc is not available for package DESeq2 Any suggestions would be greatly appreciated. to your account. What is the output of. You are doing something very wrong when installing your packages. rev2023.3.3.43278. Is there anyone the same as mine error while loading library(DESeq2)? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 4. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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. 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 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 To add to this, I have also been using DESeq2 recently and ran into the same problem. 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. 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. 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? To learn more, see our tips on writing great answers. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): If you have a query related to it or one of the replies, start a new topic and refer back with a link. a, There are binary versions available but the source versions are later: Choose Yes. When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. Running under: Windows 10 x64 (build 18362), locale: problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied, BiocManager::install("XML") Just updated my previous R to 4.01 and now I cant load DESeq2. Why do academics stay as adjuncts for years rather than move around? [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. but when I go to load the libraries I get this error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :