In install.packages() : DESeq2_2301_76497647-CSDN I can download DESeq2 using, User Agreement and Privacy Platform: x86_64-w64-mingw32/x64 (64-bit) rev2023.3.3.43278. Error: package or namespace load failed, object not found Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open 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. 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. If not fixed, Try removing remove.packages (rlang) then. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Connect and share knowledge within a single location that is structured and easy to search. 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. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: privacy statement. 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!!! One solution is to find all available packages. No error messages are returned. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. [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: Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Any suggestions would be greatly appreciated. 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. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Retrying with flexible solve.Solving environment: Found conflicts! Running under: macOS Sierra 10.12.3, locale: If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Choose Yes. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 When an R package depends on a newer package version, the required package is downloaded but not loaded. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). error: object 'rlang_dots_list' not found 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. I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Statistics ; Algorithm(ML, DL,.) now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Learn more about Stack Overflow the company, and our products. C:\R\R-3.4.3\library). Installing package(s) 'XML' Platform: x86_64-apple-darwin17.0 (64-bit) Find centralized, trusted content and collaborate around the technologies you use most. To learn more, see our tips on writing great answers. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. library(caret) namespace load failed Object sigma not Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? May be the version has problem How can I do ? I thought that working in a new environment would help, but it didnt. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): I was assuming that to be the case. [16] phyloseq1.30.0, loaded via a namespace (and not attached): Platform: x86_64-apple-darwin13.4.0 (64-bit) [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 R| - Please read the posting [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: rev2023.3.3.43278. [7] edgeR_3.16.5 limma_3.30.12 now when I tried installing the missing packages they did install. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, 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 your account. [5] IRanges_2.8.1 S4Vectors_0.12.1 I hope you can see something I can't see and help me solving this issue. 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: Already on GitHub? Policy. I tried to download the "locfit" package but I can't find it anywhere. I even tried BiocManager::install("XML") but all failed as shown below. Why is there a voltage on my HDMI and coaxial cables? As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Citation (from within R, Installing package(s) 'GenomeInfoDbData' I tried following the instructions for 2019.7 as well and I am getting the same error. + ), update = TRUE, ask = FALSE) Documentation package xfun successfully unpacked and MD5 sums checked Thanks for contributing an answer to Stack Overflow! @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. 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"). Please try reinstalling rlang on a fresh session. 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. Warning: cannot remove prior installation of package xfun I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. @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. To resolve this error, install the required package as a cluster-installed library. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' When an R package depends on a newer package version, the required package is downloaded but not loaded. 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 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [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. Running under: macOS Catalina 10.15.3, Matrix products: default Rload failed - Give up and run everything from the "permitted" library location (e.g. 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 Old packages: 'RcppArmadillo', 'survival' 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 [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 there is no package called Hmisc. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Asking for help, clarification, or responding to other answers. Making statements based on opinion; back them up with references or personal experience. install.packages ("zip") The package has place the R version constraint. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 And finally, install the problem packages, perhaps also DESeq2. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Content type 'application/zip' length 233860 bytes (228 KB) 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. Why is this sentence from The Great Gatsby grammatical? 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 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 I highly recommend that any R/RStudio version not installed inside conda be removed. Erasmus+ funds available! Does a summoned creature play immediately after being summoned by a ready action? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 May I know is there any other approach I can try? Use of this site constitutes acceptance of our User Agreement and Privacy After 3-4 manual installs everything worked. Do I need a thermal expansion tank if I already have a pressure tank? 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'. Disconnect between goals and daily tasksIs it me, or the industry? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [13] ggplot23.3.0 car3.0-7 carData3.0-3 Not the answer you're looking for? 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 . it would be good to hear any speculation you have of how this might have happened). sessionInfo() 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. to allow custom library locations. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 @artembus Sounds like it was a ton of work! If you preorder a special airline meal (e.g. Should I update the Bioconductor to latest version instead? Is there a proper earth ground point in this switch box? guide. [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: 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 do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 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. Well occasionally send you account related emails. installation of package GenomeInfoDbData had non-zero exit status. .onLoad failed in loadNamespace() for 'rlang', details: Sounds like you might have an issue with which R Rstudio is running. 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Why do academics stay as adjuncts for years rather than move around? Does anyone know why I'm getting the following message when I load tidyverse in a new session. I also tried something I found on google: but the installation had errors too, I can write them here if needed. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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. I'm having a similar error, but different package: library("DESeq2") Join us at CRISPR workshops in Koper, Slovenia in 2023. Please remember to confirm an answer once you've received one. 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 incident has nothing to do with me; can I use this this way? Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat - the incident has nothing to do with me; can I use this this way? We've tried this - and can replicate this issue on a completely new install with no existing package installs. DESeq2 installation in R - Bioconductor Try again and choose No. How to notate a grace note at the start of a bar with lilypond? 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' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: Policy. Use MathJax to format equations. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: As such there are two solutions that may be more or less attainable given your own IT system. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 I've copied the output below in case it helps with troubleshooting. Traffic: 307 users visited in the last hour, I am new to all this! Glad everything is finally working now. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Resolving package or namespace loading error Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Feedback Warning message: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Language(R, Python, SQL) When you load the package, you can observe this error. Loading required package: GenomeInfoDb But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 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. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib biocLite(), install.packages() (and the devtools equivalent?) Just updated my previous R to 4.01 and now I cant load DESeq2. How do I align things in the following tabular environment? What do I need to do to reproduce your problem? downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in R version 3.6.3 (2020-02-29) [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. DESeq2 - I can't get the library to load - Bioconductor 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. Looking for incompatible packages. or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. The other option is to download and older version of locfit from the package archive and install manually. How can I fix error with loading package in R ? | ResearchGate Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 2. What is the output of. 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. 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. Is a PhD visitor considered as a visiting scholar? Connect and share knowledge within a single location that is structured and easy to search. Open Source Biology & Genetics Interest Group. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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. :), BiocManager::install("locift") March 1, 2023, 4:56pm The error states that the current version is 0.4.5 but 0.4.10 is required. 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 Use of this site constitutes acceptance of our User Agreement and Privacy 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. Is there anyone the same as mine error while loading library(DESeq2)? [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Press CTRL-C to abort. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 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 . ()library(DESeq2):Error in loadNamespace: no package called ""s Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers.