Please remember to confirm an answer once you've received one. I tried again and again was met with missing packages BUT!!! Platform: x86_64-apple-darwin13.4.0 (64-bit) It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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. If not fixed, Try removing remove.packages (rlang) then. library(caret) namespace load failed Object sigma not found caret , . No error messages are returned. rev2023.3.3.43278. and then updating the packages that command indicates. [16] phyloseq1.30.0, loaded via a namespace (and not attached): I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE biocLite(), install.packages() (and the devtools equivalent?) To subscribe to this RSS feed, copy and paste this URL into your RSS reader. The other option is to download and older version of locfit from the package archive and install manually. Making statements based on opinion; back them up with references or personal experience. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Platform: x86_64-apple-darwin17.0 (64-bit) Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Not the answer you're looking for? 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. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) (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 . 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. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. When you load the package, you can observe this error. March 1, 2023, 4:56pm Use this. Use of this site constitutes acceptance of our User Agreement and Privacy requires R 4 and running more than a couple of releases behind in R risks multiplying problems. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Remember to always click on the red Show me the content on this page notice when navigating these older versions. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 so I would try to use BiocManager::install("XML"). [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Statistics ; Algorithm(ML, DL,.) I was assuming that to be the case. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Content type 'application/zip' length 233860 bytes (228 KB) - the incident has nothing to do with me; can I use this this way? 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!!! [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Have you tried install.packages("locfit") ? 2. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. 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 Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? 9. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 1. 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. Do I need a thermal expansion tank if I already have a pressure tank? 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 downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. So, supposedly the issue is with Hmisc. I have tried your suggestion and also updating the packages that command indicates. now when I tried installing the missing packages they did install. 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. Solving environment: Found conflicts! 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. Update all/some/none? downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked How to use Slater Type Orbitals as a basis functions in matrix method correctly? In install.packages() : It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. C:\R\R-3.4.3\library). 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. Are you sure the R you're running from the command line is installed through Anaconda as well? install.packages("BiocManager"), I get this error: 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 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'. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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 ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . How can we prove that the supernatural or paranormal doesn't exist? [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Running under: macOS Catalina 10.15.3, Matrix products: default So if you still get this error try changing your CRAN mirror. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Sign up for a free GitHub account to open an issue and contact its maintainers and the community. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Whats the grammar of "For those whose stories they are"? Sorry, I'm newbie. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I tried following the instructions for 2019.7 as well and I am getting the same error. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Running under: macOS Sierra 10.12.6. Find centralized, trusted content and collaborate around the technologies you use most. Citation (from within R, to your account. This can take several minutes. Open Source Biology & Genetics Interest Group. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Platform: x86_64-apple-darwin15.6.0 (64-bit) 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 If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [a/s/n]: Join us at CRISPR workshops in Koper, Slovenia in 2023. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 From the console install.packages ("rlang") should fix this. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages 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: install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR I've copied the output below in case it helps with troubleshooting. Sounds like there might be an issue with conda setup? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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: Just updated my previous R to 4.01 and now I cant load DESeq2. But I guess you have many problems with your installation, and I'd suggest. A place where magic is studied and practiced? By clicking Sign up for GitHub, you agree to our terms of service and Then I reinstalled R then Rstudio then RTools. I can download DESeq2 using, User Agreement and Privacy vegan) just to try it, does this inconvenience the caterers and staff? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. This article explains how to resolve the package or namespace loading error. Is a PhD visitor considered as a visiting scholar? Surly Straggler vs. other types of steel frames. What am I doing wrong here in the PlotLegends specification? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Whats the grammar of "For those whose stories they are"? The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): And finally, install the problem packages, perhaps also DESeq2. I'm having a similar error, but different package: library("DESeq2") [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Why do academics stay as adjuncts for years rather than move around? Why do academics stay as adjuncts for years rather than move around? /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Asking for help, clarification, or responding to other answers. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. To view documentation for the version of this package installed I'm trying to reproduce your problem, so being as precise as possible is important. Hello, Looking for incompatible packages.This can take several minutes. Connect and share knowledge within a single location that is structured and easy to search. Connect and share knowledge within a single location that is structured and easy to search. Warning message: Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Policy. Is the God of a monotheism necessarily omnipotent? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) What do I need to do to reproduce your problem? error: object 'rlang_dots_list' not found Is there anything I can do to speed it up? Loading required package: GenomeInfoDb First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Installing Hmisc as suggested above did not solve the issue. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 "4.2") and enter: For older versions of R, please refer to the appropriate You signed in with another tab or window. 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 + "htmlTable", "xfun" But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Did you do that? I would recommend installing an older version of QIIME 2 for this plugin to work. Find centralized, trusted content and collaborate around the technologies you use most. What is the output of. How do I align things in the following tabular environment? 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. Is a PhD visitor considered as a visiting scholar? Policy. Styling contours by colour and by line thickness in QGIS. Policy. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. 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 'XML' so I would try to use BiocManager::install ("XML"). [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 package rlang was built under R version 3.5.1. Policy. Use of this site constitutes acceptance of our User Agreement and Privacy New replies are no longer allowed. Well occasionally send you account related emails. Running. [7] edgeR_3.16.5 limma_3.30.12 As such there are two solutions that may be more or less attainable given your own IT system. ERROR: dependency Hmisc is not available for package DESeq2 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. rev2023.3.3.43278. Language(R, Python, SQL) Content type 'application/zip' length 4255589 bytes (4.1 MB) sessionInfo() Is there anyone the same as mine error while loading library(DESeq2)? [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 This includes any installed libraries. I also tried something I found on google: but the installation had errors too, I can write them here if needed. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Surly Straggler vs. other types of steel frames. 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Content type 'application/zip' length 386703 bytes (377 KB) When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. Installation instructions to use this How to notate a grace note at the start of a bar with lilypond? [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 When you load the package, you can observe this error. March 1, 2023, 7:31pm Post questions about Bioconductor there is no package called locfit. Why is there a voltage on my HDMI and coaxial cables? One solution is to find all available packages. To learn more, see our tips on writing great answers. @artembus Sounds like it was a ton of work! [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: Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Sign in Press CTRL-C to abort. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: 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: I even tried BiocManager::install("XML") but all failed as shown below. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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 It only takes a minute to sign up. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Choose Yes. 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. Thanks for contributing an answer to Bioinformatics Stack Exchange! Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? After 3-4 manual installs everything worked. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. .onLoad failed in loadNamespace() for 'rlang', details: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Start R to confirm they are gone. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [7] datasets methods base, other attached packages: locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 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 . binary source needs_compilation - the incident has nothing to do with me; can I use this this way? binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 library(DESeq2) If you have a query related to it or one of the replies, start a new topic and refer back with a link. Connect and share knowledge within a single location that is structured and easy to search. library(DESeq2) R version 3.6.3 (2020-02-29) To resolve this error, install the required package as a cluster-installed library. In file.copy(savedcopy, lib, recursive = TRUE) : Why do many companies reject expired SSL certificates as bugs in bug bounties? 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. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. The best answers are voted up and rise to the top, Not the answer you're looking for? Documentation 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. Why are physically impossible and logically impossible concepts considered separate in terms of probability? Running under: Windows 10 x64 (build 18362), locale: Is there a single-word adjective for "having exceptionally strong moral principles"? 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]]):
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