Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. @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 I run install.packages(GenomeInfoDb) from R console, it is telling me that the package is not available for R version 3.5.1. Running. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Is a PhD visitor considered as a visiting scholar? Why is there a voltage on my HDMI and coaxial cables? Fortunately I was able to solve it by doing things from several suggested solutions. Any other suggestion? 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. install.packages("BiocManager"), I get this error: 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. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Looking for incompatible packages.This can take several minutes. 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. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 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 installed the package successfully with conda, but Rstudio is apparently does not know about it. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Just updated my previous R to 4.01 and now I cant load DESeq2. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Whats the grammar of "For those whose stories they are"? Press CTRL-C to abort. Open Source Biology & Genetics Interest Group. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. rev2023.3.3.43278. Not the answer you're looking for? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. rev2023.3.3.43278. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 R version 4.0.1 (2020-06-06) I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Solution To resolve this error, install the required package as a cluster-installed library. This topic was automatically closed 21 days after the last reply. 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. Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Installation instructions to use this 1. 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. Policy. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Update all/some/none? I'm trying to reproduce your problem, so being as precise as possible is important. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Powered by Discourse, best viewed with JavaScript enabled, DESeq2: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Error: package GenomeInfoDb could not be loaded. 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. Disconnect between goals and daily tasksIs it me, or the industry? [a/s/n]: C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). May be the version has problem How can I do ? Thanks for contributing an answer to Stack Overflow! MathJax reference. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? The package has place the R version constraint. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Policy. 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. If you try loading the DEseq2 library now, that might work. Policy. Is there anyone the same as mine error while loading library(DESeq2)? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Not the answer you're looking for? [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Thank you @hharder. library(caret) namespace load failed Object sigma not 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). So, supposedly the issue is with Hmisc. Asking for help, clarification, or responding to other answers. Thanks for contributing an answer to Stack Overflow! and then updating the packages that command indicates. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked there is no package called Hmisc. Learn more about Stack Overflow the company, and our products. Bioconductor release. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. As such there are two solutions that may be more or less attainable given your own IT system. Surly Straggler vs. other types of steel frames. More info about Internet Explorer and Microsoft Edge. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Traffic: 307 users visited in the last hour, I am new to all this! Feedback Well occasionally send you account related emails. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. so I would try to use BiocManager::install("XML"). If you have a query related to it or one of the replies, start a new topic and refer back with a link. Making statements based on opinion; back them up with references or personal experience. 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. Does anyone know why I'm getting the following message when I load tidyverse in a new session. May I know is there any other approach I can try? Follow Up: struct sockaddr storage initialization by network format-string. Can't Load R DESeq2 Library, Installed All Missing Packages and Still I can download DESeq2 using, User Agreement and Privacy 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Language(R, Python, SQL) March 1, 2023, 3:25pm Installing package(s) 'XML' BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib One solution is to find all available packages. Platform: x86_64-apple-darwin13.4.0 (64-bit) A place where magic is studied and practiced? enter citation("DESeq2")): To install this package, start R (version Running under: Windows 10 x64 (build 18362), locale: if (!require("BiocManager", quietly = TRUE)) I would recommend installing an older version of QIIME 2 for this plugin to work. I then launched the R application (from the finder, not RStudio) and installed BiocManager. package rlang was built under R version 3.5.1. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? "After the incident", I started to be more careful not to trip over things. now when I tried installing the missing packages they did install. So if you still get this error try changing your CRAN mirror. 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'. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. If you preorder a special airline meal (e.g. New replies are no longer allowed. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Post questions about Bioconductor You are doing something very wrong when installing your packages. Warning message: In install.packages() : sessionInfo() Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Content type 'application/zip' length 386703 bytes (377 KB) Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. 9. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: vegan) just to try it, does this inconvenience the caterers and staff? [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 I tried to get a whole new environment and install an old version of Qiime but I still got a ton of conflicts and it didnt install. March 1, 2023, 7:31pm And finally, install the problem packages, perhaps also DESeq2. Give up and run everything from the "permitted" library location (e.g. package xfun successfully unpacked and MD5 sums checked LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: 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]]) : 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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
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