error: package or namespace load failed for 'deseq2 error: package or namespace load failed for 'deseq2

How to use Slater Type Orbitals as a basis functions in matrix method correctly? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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'. We've tried this - and can replicate this issue on a completely new install with no existing package installs. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Is there a proper earth ground point in this switch box? You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [13] ggplot23.3.0 car3.0-7 carData3.0-3 Use of this site constitutes acceptance of our User Agreement and Privacy Whats the grammar of "For those whose stories they are"? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? 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. Policy. [69] tidyselect_1.0.0. I would like to install DESeq2 for DE analysis. Content type 'application/zip' length 386703 bytes (377 KB) 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. 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 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. Replacing broken pins/legs on a DIP IC package. 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. I thought that working in a new environment would help, but it didnt. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Sign in Why is this sentence from The Great Gatsby grammatical? I tried again and again was met with missing packages BUT!!! Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. library(DESeq2) You signed in with another tab or window. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. [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: It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [1] stats4 parallel stats graphics grDevices utils 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. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 R version 4.0.1 (2020-06-06) It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Should I update the Bioconductor to latest version instead? Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Following successful installation of backports BiocManager::install ("DESeq2") will succeed under [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Thanks! Let me confer with the team. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Warning message: Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Join us at CRISPR workshops in Koper, Slovenia in 2023. Documentation So, supposedly the issue is with Hmisc. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 ERROR: dependency Hmisc is not available for package DESeq2 Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Just to add on -- do you require an old version of Bioconductor for your current project? Not the answer you're looking for? To view documentation for the version of this package installed To resolve this error, install the required package as a cluster-installed library. Installing Hmisc as suggested above did not solve the issue. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. To learn more, see our tips on writing great answers. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Platform: x86_64-apple-darwin13.4.0 (64-bit) [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Please try the following steps: Quit all R/Rstudio sessions. Press CTRL-C to abort. Old packages: 'RcppArmadillo', 'survival' Use of this site constitutes acceptance of our User Agreement and Privacy Loading required package: GenomeInfoDb [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Thanks for contributing an answer to Bioinformatics Stack Exchange! [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 When you load the package, you can observe this error. Also note, however, that the error you got has been associated in the past with mirror outages. If you try loading the DEseq2 library now, that might work. Follow Up: struct sockaddr storage initialization by network format-string. I'm trying to reproduce your problem, so being as precise as possible is important. Disconnect between goals and daily tasksIs it me, or the industry? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Content type 'application/zip' length 233860 bytes (228 KB) 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc One solution is to find all available packages. Have a question about this project? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. 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. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. installation of package GenomeInfoDbData had non-zero exit status. Use of this site constitutes acceptance of our User Agreement and Privacy Whats the grammar of "For those whose stories they are"? now when I tried installing the missing packages they did install. - the incident has nothing to do with me; can I use this this way? [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Just updated my previous R to 4.01 and now I cant load DESeq2. How can we prove that the supernatural or paranormal doesn't exist? 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). A place where magic is studied and practiced? When you load the package, you can observe this error. so I would try to use BiocManager::install("XML"). Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Does a summoned creature play immediately after being summoned by a ready action? [16] phyloseq1.30.0, loaded via a namespace (and not attached): [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 [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: rev2023.3.3.43278. How do I align things in the following tabular environment? but when I go to load the libraries I get this error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : sessionInfo() @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. 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. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. there is no package called Hmisc. Running under: macOS Catalina 10.15.3, Matrix products: default Error: package GenomeInfoDb could not be loaded. What do I need to do to reproduce your problem? dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext If not fixed, Try removing remove.packages (rlang) then. Looking for incompatible packages. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. And finally, install the problem packages, perhaps also DESeq2. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 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 just figured Id ask. I've copied the output below in case it helps with troubleshooting. it would be good to hear any speculation you have of how this might have happened). if (!require("BiocManager", quietly = TRUE)) [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 I do know that it works well in qiime2-2020.6. When an R package depends on a newer package version, the required package is downloaded but not loaded. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( @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. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 package in your R session. privacy statement. rev2023.3.3.43278. Warning message: That plugin is has not been updated to work with later releases of QIIME 2. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 nnet, spatial, survival installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. 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). "4.2") and enter: For older versions of R, please refer to the appropriate 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. there is no package called Hmisc. Making statements based on opinion; back them up with references or personal experience. Thanks for contributing an answer to Stack Overflow! 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? Just realize that I need to write the script "library("DESeq2")" before I proceed. Installing package(s) 'XML' Not the answer you're looking for? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 running multiple versions of the same package, keeping separate libraries for some projects). By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Update all/some/none? 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 . Post questions about Bioconductor Already on GitHub? Styling contours by colour and by line thickness in QGIS. I was assuming that to be the case. there is no package called locfit. What am I doing wrong here in the PlotLegends specification? This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 + "htmlTable", "xfun" I am running a new install of R (3.5.0) and RStudio (1.1.414). to allow custom library locations. Installing package(s) 'htmlTable', 'xfun' [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Installing package(s) 'GenomeInfoDbData' Connect and share knowledge within a single location that is structured and easy to search. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Any suggestions would be greatly appreciated. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 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]]): I even tried BiocManager::install("XML") but all failed as shown below. R version 3.6.3 (2020-02-29) Sounds like you might have an issue with which R Rstudio is running. March 1, 2023, 4:56pm 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 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Erasmus+ funds available! Solving environment: Found conflicts! binary source needs_compilation Why is there a voltage on my HDMI and coaxial cables? Well occasionally send you account related emails. New replies are no longer allowed. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Try installing zip, and then loading olsrr. 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. Use this. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. By clicking Sign up for GitHub, you agree to our terms of service and I highly recommend that any R/RStudio version not installed inside conda be removed. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 May I know is there any other approach I can try? You are doing something very wrong when installing your packages. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 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). Find centralized, trusted content and collaborate around the technologies you use most. I hope you can see something I can't see and help me solving this issue. Do I need a thermal expansion tank if I already have a pressure tank? install.packages ("zip") I also tried something I found on google: but the installation had errors too, I can write them here if needed. From the console install.packages ("rlang") should fix this. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 ERROR: lazy loading failed for package Hmisc downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. "htmlTable", "xfun" I installed the package successfully with conda, but Rstudio is apparently does not know about it. If you have a query related to it or one of the replies, start a new topic and refer back with a link. March 1, 2023, 7:31pm 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. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. Are you sure the R you're running from the command line is installed through Anaconda as well? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, (Factorization). Have you tried install.packages("locfit") ? 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. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Please try reinstalling rlang on a fresh session. Citation (from within R, Also make sure that you have RTools.exe installed and working. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Looking for incompatible packages.This can take several minutes. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Installation instructions to use this Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? 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. Connect and share knowledge within a single location that is structured and easy to search. I would recommend installing an older version of QIIME 2 for this plugin to work. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? . Are there tables of wastage rates for different fruit and veg? [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [a/s/n]: [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? May be the version has problem How can I do ? Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. MathJax reference. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib [7] edgeR_3.16.5 limma_3.30.12 "After the incident", I started to be more careful not to trip over things. This can take several minutes. Feedback there is no package called data.table [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 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. Acidity of alcohols and basicity of amines. Sorry, I'm newbie. sessionInfo() unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Start R to confirm they are gone. Give up and run everything from the "permitted" library location (e.g. I'm having a similar error, but different package: library("DESeq2") package rlang was built under R version 3.5.1. 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").