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. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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 As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Citation (from within R, Connect and share knowledge within a single location that is structured and easy to search. As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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. now when I tried installing the missing packages they did install. "htmlTable", "xfun" [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Is there a single-word adjective for "having exceptionally strong moral principles"? 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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"). install.packages("BiocManager"), I get this error: Use of this site constitutes acceptance of our User Agreement and Privacy Let me confer with the team. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Thnaks anyway, Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems, How Intuit democratizes AI development across teams through reusability. The best answers are voted up and rise to the top, Not the answer you're looking for? Any other suggestion? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 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!!! 2. What is the output of. Error: package or namespace load failed for 'DESeq2 - Bioconductor If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Whats the grammar of "For those whose stories they are"? But I guess you have many problems with your installation, and I'd suggest. Update all/some/none? Old packages: 'RcppArmadillo', 'survival' Thank you @hharder. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages I tried to download the "locfit" package but I can't find it anywhere. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. After 3-4 manual installs everything worked. March 1, 2023, 7:31pm Error: package GenomeInfoDb could not be loaded. Is there a proper earth ground point in this switch box? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Solving environment: Found conflicts! + ), update = TRUE, ask = FALSE) [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Convince your IT department to relax the permissions for R packages /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Not the answer you're looking for? What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. If you try loading the DEseq2 library now, that might work. Is a PhD visitor considered as a visiting scholar? Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: 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. 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. DESeq2 - I can't get the library to load - Bioconductor To learn more, see our tips on writing great answers. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked vegan) just to try it, does this inconvenience the caterers and staff? Open Source Biology & Genetics Interest Group. sessionInfo() Running. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Loading required package: GenomeInfoDb Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. I even tried BiocManager::install("XML") but all failed as shown below. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Also make sure that you have RTools.exe installed and working. 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. there is no package called Hmisc. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 March 1, 2023, 3:25pm "After the incident", I started to be more careful not to trip over things. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Can't Load R DESeq2 Library, Installed All Missing Packages and Still I tried again and again was met with missing packages BUT!!! enter citation("DESeq2")): To install this package, start R (version The other option is to download and older version of locfit from the package archive and install manually. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, What do I need to do to reproduce your problem? guide. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 I've copied the output below in case it helps with troubleshooting. I hope you can see something I can't see and help me solving this issue. From the console install.packages ("rlang") should fix this. 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. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. How to use Slater Type Orbitals as a basis functions in matrix method correctly? .onLoad failed in loadNamespace() for 'rlang', details: [7] edgeR_3.16.5 limma_3.30.12 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") - the incident has nothing to do with me; can I use this this way? I was assuming that to be the case. @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. When you load the package, you can observe this error. library (olsrr) - Error - General - RStudio Community March 1, 2023, 4:56pm rev2023.3.3.43278. Asking for help, clarification, or responding to other answers. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? How do I align things in the following tabular environment? [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Thanks for contributing an answer to Stack Overflow! 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. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. I am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. Making statements based on opinion; back them up with references or personal experience. 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. Did you do that? there is no package called Hmisc. DESeq2 installation in R - Bioconductor So, supposedly the issue is with Hmisc. Installing package(s) 'GenomeInfoDbData' so I would try to use BiocManager::install("XML"). The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. 9. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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. Is there anyone the same as mine error while loading library(DESeq2)? 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 . But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () In file.copy(savedcopy, lib, recursive = TRUE) : requires R 4 and running more than a couple of releases behind in R risks multiplying problems. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Not the answer you're looking for? Content type 'application/zip' length 233860 bytes (228 KB) [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Then I reinstalled R then Rstudio then RTools. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. March 1, 2023, 8:52pm Is the God of a monotheism necessarily omnipotent? CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. Remember to always click on the red Show me the content on this page notice when navigating these older versions. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR 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") I then launched the R application (from the finder, not RStudio) and installed BiocManager. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Looking for incompatible packages.This can take several minutes. I also tried something I found on google: but the installation had errors too, I can write them here if needed. Platform: x86_64-apple-darwin15.6.0 (64-bit) Follow Up: struct sockaddr storage initialization by network format-string. Acidity of alcohols and basicity of amines. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 package rlang was built under R version 3.5.1. How can I fix error with loading package in R ? | ResearchGate A place where magic is studied and practiced? 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. [5] IRanges_2.8.1 S4Vectors_0.12.1 @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. - the incident has nothing to do with me; can I use this this way? Policy. And finally, install the problem packages, perhaps also DESeq2. Why is this sentence from The Great Gatsby grammatical? Use MathJax to format equations. Just realize that I need to write the script "library("DESeq2")" before I proceed. . (I have the most recent version of tidyverse, RStudio, and R.) Error: package or namespace load failed for 'tidyverse': .onAttach failed in attachNamespace() for 'tidyverse', details: call: glue(str, .envir = .envir, .transformer = transformer . [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 To resolve this error, install the required package as a cluster-installed library. Disconnect between goals and daily tasksIs it me, or the industry? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Have a question about this project? [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Glad everything is finally working now. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other.
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