error: package or namespace load failed for 'deseq2

I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Content type 'application/zip' length 386703 bytes (377 KB) + "htmlTable", "xfun" Warning message: Citation (from within R, Is there a proper earth ground point in this switch box? March 1, 2023, 8:52pm 9. 4. Use of this site constitutes acceptance of our User Agreement and Privacy Installing package(s) 'GenomeInfoDbData' sessionInfo() 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 [69] tidyselect_1.0.0. Policy. 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Use of this site constitutes acceptance of our User Agreement and Privacy Platform: x86_64-apple-darwin15.6.0 (64-bit) To resolve this error, install the required package as a cluster-installed library. And finally, install the problem packages, perhaps also DESeq2. Use MathJax to format equations. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Documentation Use of this site constitutes acceptance of our User Agreement and Privacy Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Making statements based on opinion; back them up with references or personal experience. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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"). Platform: x86_64-w64-mingw32/x64 (64-bit) A place where magic is studied and practiced? Why are physically impossible and logically impossible concepts considered separate in terms of probability? 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 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. March 1, 2023, 4:56pm It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. @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. Is the God of a monotheism necessarily omnipotent? Erasmus+ funds available! there is no package called data.table 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 . 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. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Content type 'application/zip' length 4255589 bytes (4.1 MB) nnet, spatial, survival. Warning: restored xfun, The downloaded binary packages are in I have tried your suggestion and also updating the packages that command indicates. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. rev2023.3.3.43278. Traffic: 307 users visited in the last hour, I am new to all this! What do I need to do to reproduce your problem? Already on GitHub? Not the answer you're looking for? [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: 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): .onLoad failed in loadNamespace() for 'rlang', details: Running. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Making statements based on opinion; back them up with references or personal experience. I thought that working in a new environment would help, but it didnt. library(DESeq2) Follow Up: struct sockaddr storage initialization by network format-string. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Surly Straggler vs. other types of steel frames. Have a question about this project? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. This article explains how to resolve the package or namespace loading error. Connect and share knowledge within a single location that is structured and easy to search. Replacing broken pins/legs on a DIP IC package. I can download DESeq2 using, User Agreement and Privacy Also note, however, that the error you got has been associated in the past with mirror outages. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): More info about Internet Explorer and Microsoft Edge. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Surly Straggler vs. other types of steel frames. I would recommend installing an older version of QIIME 2 for this plugin to work. 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'. I tried again and again was met with missing packages BUT!!! By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Warning message: library(caret) namespace load failed Object sigma not found caret , . [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 No error messages are returned. Is there anything I can do to speed it up? Is there a single-word adjective for "having exceptionally strong moral principles"? + ), update = TRUE, ask = FALSE) Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? [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: data . Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Give up and run everything from the "permitted" library location (e.g. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 [7] edgeR_3.16.5 limma_3.30.12 [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 there is no package called GenomeInfoDbData Remember to always click on the red Show me the content on this page notice when navigating these older versions. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 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 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). 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? Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? @artembus Sounds like it was a ton of work! 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. What am I doing wrong here in the PlotLegends specification? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. By clicking Sign up for GitHub, you agree to our terms of service and and then updating the packages that command indicates. Just updated my previous R to 4.01 and now I cant load DESeq2. I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. Why do academics stay as adjuncts for years rather than move around? [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 After 3-4 manual installs everything worked. 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. 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 [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). How can we prove that the supernatural or paranormal doesn't exist? Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. If you try loading the DEseq2 library now, that might work. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Update all/some/none? Are there tables of wastage rates for different fruit and veg? Connect and share knowledge within a single location that is structured and easy to search. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 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 . Running under: Windows 10 x64 (build 18362), locale: Thanks for contributing an answer to Stack Overflow! error: object 'rlang_dots_list' not found In install.packages() : Try again and choose No. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Warning: cannot remove prior installation of package xfun downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Policy. binary source needs_compilation [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Loading required package: GenomicRanges In addition: Warning message: Whats the grammar of "For those whose stories they are"? [5] IRanges_2.8.1 S4Vectors_0.12.1 What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? guide. This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Did you do that? Running under: macOS Sierra 10.12.6. It is working now. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. March 1, 2023, 3:25pm [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Choose Yes. Making statements based on opinion; back them up with references or personal experience. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. If you have a query related to it or one of the replies, start a new topic and refer back with a link. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( May I know is there any other approach I can try? [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Why do academics stay as adjuncts for years rather than move around? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. ERROR: lazy loading failed for package Hmisc there is no package called Hmisc. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Any suggestions would be greatly appreciated. Join us at CRISPR workshops in Koper, Slovenia in 2023. Solving environment: Found conflicts! I tried to download the "locfit" package but I can't find it anywhere. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. I guess that means we can finally close this issue. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. When you load the package, you can observe this error. if (!require("BiocManager", quietly = TRUE)) 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. 2. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Retrying with flexible solve.Solving environment: Found conflicts! package rlang was built under R version 3.5.1. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Any other suggestion? Does a summoned creature play immediately after being summoned by a ready action? Statistics ; Algorithm(ML, DL,.) Installing package(s) 'htmlTable', 'xfun' 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. As such there are two solutions that may be more or less attainable given your own IT system. To learn more, see our tips on writing great answers. [7] datasets methods base, other attached packages: Please try reinstalling rlang on a fresh session. "After the incident", I started to be more careful not to trip over things. R version 3.6.3 (2020-02-29) [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [1] stats4 parallel stats graphics grDevices utils I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Also make sure that you have RTools.exe installed and working. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 If you preorder a special airline meal (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.

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