error: package or namespace load failed for 'deseq2

[13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 New replies are no longer allowed. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). R version 4.0.1 (2020-06-06) [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 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 The package has place the R version constraint. By clicking Sign up for GitHub, you agree to our terms of service and Sounds like you might have an issue with which R Rstudio is running. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Whats the grammar of "For those whose stories they are"? Thanks for contributing an answer to Stack Overflow! To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib and then updating the packages that command indicates. Platform: x86_64-apple-darwin17.0 (64-bit) Warning message: Is a PhD visitor considered as a visiting scholar? dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. What is a word for the arcane equivalent of a monastery? unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Making statements based on opinion; back them up with references or personal experience. 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. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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 Solving environment: Found conflicts! 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. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Thanks! Old packages: 'RcppArmadillo', 'survival' 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. there is no package called Hmisc. Not the answer you're looking for? As such there are two solutions that may be more or less attainable given your own IT system. 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. Thanks for your suggestion. 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: library(caret) namespace load failed Object sigma not found caret , . Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. rev2023.3.3.43278. 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? 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. A place where magic is studied and practiced? 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'. installation of package GenomeInfoDbData had non-zero exit status. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Policy. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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. 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. I'm having a similar error, but different package: library("DESeq2") I'm trying to reproduce your problem, so being as precise as possible is important. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. You signed in with another tab or window. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Policy. 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"). I then launched the R application (from the finder, not RStudio) and installed BiocManager. May I know is there any other approach I can try? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. 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 Looking for incompatible packages.This can take several minutes. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 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"). [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 I have tried your suggestion and also updating the packages that command indicates. - the incident has nothing to do with me; can I use this this way? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. data . Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. How do you ensure that a red herring doesn't violate Chekhov's gun? Try installing zip, and then loading olsrr. 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. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. error: object 'rlang_dots_list' not found 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). ERROR: dependency Hmisc is not available for package DESeq2 Remember to always click on the red Show me the content on this page notice when navigating these older versions. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. Warning message: /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Asking for help, clarification, or responding to other answers. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Fortunately I was able to solve it by doing things from several suggested solutions. R version 3.6.3 (2020-02-29) [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. 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 When you load the package, you can observe this error. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Running under: macOS Catalina 10.15.3, Matrix products: default Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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 . "htmlTable", "xfun" I guess that means we can finally close this issue. This can take several minutes. Platform: x86_64-w64-mingw32/x64 (64-bit) In addition: Warning message: Does a summoned creature play immediately after being summoned by a ready action? From the console install.packages ("rlang") should fix this. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Hello, Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Are you sure the R you're running from the command line is installed through Anaconda as well? binary source needs_compilation 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 Policy. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. That plugin is has not been updated to work with later releases of QIIME 2. [16] phyloseq1.30.0, loaded via a namespace (and not attached): 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 Connect and share knowledge within a single location that is structured and easy to search. 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. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. 4. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Try again and choose No. Why do academics stay as adjuncts for years rather than move around? Making statements based on opinion; back them up with references or personal experience. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. I thought that working in a new environment would help, but it didnt. 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. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Replacing broken pins/legs on a DIP IC package. .onLoad failed in loadNamespace() for 'rlang', details: [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Retrying with flexible solve.Solving environment: Found conflicts! 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. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. sessionInfo() in your system, start R and enter: Follow The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). MathJax reference. [69] tidyselect_1.0.0. Well occasionally send you account related emails. I tried again and again was met with missing packages BUT!!! . Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Already on GitHub? Why do academics stay as adjuncts for years rather than move around? What am I doing wrong here in the PlotLegends specification? Installing package(s) 'GenomeInfoDbData' * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Have a question about this project? March 1, 2023, 8:52pm The best answers are voted up and rise to the top, Not the answer you're looking for? So, supposedly the issue is with Hmisc. To resolve this error, install the required package as a cluster-installed library. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 [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: Also note, however, that the error you got has been associated in the past with mirror outages. Join us at CRISPR workshops in Koper, Slovenia in 2023. Should I update the Bioconductor to latest version instead? guide. Installation instructions to use this to your account. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Please try the following steps: Quit all R/Rstudio sessions. library(DESeq2) How to notate a grace note at the start of a bar with lilypond? It is working now. Use of this site constitutes acceptance of our User Agreement and Privacy Making statements based on opinion; back them up with references or personal experience. Sounds like there might be an issue with conda setup? (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 .
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