error: package or namespace load failed for 'deseq2

- the incident has nothing to do with me; can I use this this way? Just to add on -- do you require an old version of Bioconductor for your current project? [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Find centralized, trusted content and collaborate around the technologies you use most. [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: Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Running under: Windows 10 x64 (build 18362), locale: Is it suspicious or odd to stand by the gate of a GA airport watching the planes? downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). there is no package called Hmisc. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 While a notebook is attached to a cluster, the R namespace cannot be refreshed. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. 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 error: object 'rlang_dots_list' not found Thank you @hharder. there is no package called locfit. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Solving environment: Found conflicts! 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. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Already on GitHub? Running under: macOS Sierra 10.12.6. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Then I reinstalled R then Rstudio then RTools. But I guess you have many problems with your installation, and I'd suggest. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. Have a question about this project? I hope you can see something I can't see and help me solving this issue. What do I need to do to reproduce your problem? Should I update the Bioconductor to latest version instead? Content type 'application/zip' length 4255589 bytes (4.1 MB) Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 1. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Thanks! [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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. Have you tried install.packages("locfit") ? [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Policy. Surly Straggler vs. other types of steel frames. Sorry if I missed this, the question was quite long so I kind of skimmed, but I noticed that early on some of the packages were reported as requiring manual compilation from source. ERROR: lazy loading failed for package Hmisc Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Thanks for contributing an answer to Stack Overflow! I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Why are physically impossible and logically impossible concepts considered separate in terms of probability? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Use of this site constitutes acceptance of our User Agreement and Privacy Platform: x86_64-w64-mingw32/x64 (64-bit) 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). [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Use this. [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. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Traffic: 307 users visited in the last hour, I am new to all this! [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 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"). now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. 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. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 so I would try to use BiocManager::install("XML"). Please try the following steps: Quit all R/Rstudio sessions. Policy. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: To subscribe to this RSS feed, copy and paste this URL into your RSS reader. @artembus Sounds like it was a ton of work! This article explains how to resolve the package or namespace loading error. [16] phyloseq1.30.0, loaded via a namespace (and not attached): 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. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R I would like to install DESeq2 for DE analysis. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 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. there is no package called Hmisc. Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. there is no package called GenomeInfoDbData [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. + "htmlTable", "xfun" [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: to your account. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") When an R package depends on a newer package version, the required package is downloaded but not loaded. 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]]): package xfun successfully unpacked and MD5 sums checked If you have a query related to it or one of the replies, start a new topic and refer back with a link. Please try reinstalling rlang on a fresh session. Installing Hmisc as suggested above did not solve the issue. May be the version has problem How can I do ? I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. I'm trying to reproduce your problem, so being as precise as possible is important. Connect and share knowledge within a single location that is structured and easy to search. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I then launched the R application (from the finder, not RStudio) and installed BiocManager. 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). 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: No error messages are returned. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Running under: macOS Catalina 10.15.3, Matrix products: default How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Why is this sentence from The Great Gatsby grammatical? R version 4.0.1 (2020-06-06) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. I'm having a similar error, but different package: library("DESeq2") 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!!! If it fails, required operating system facilities are missing. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in "After the incident", I started to be more careful not to trip over things. 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. Post questions about Bioconductor Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. - the incident has nothing to do with me; can I use this this way? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: 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. Not the answer you're looking for? To learn more, see our tips on writing great answers. 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. Does anyone know why I'm getting the following message when I load tidyverse in a new session. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Use of this site constitutes acceptance of our User Agreement and Privacy [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. rev2023.3.3.43278. Retrying with flexible solve.Solving environment: Found conflicts! This topic was automatically closed 21 days after the last reply. Warning: cannot remove prior installation of package xfun [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 library(DESeq2) 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. @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. library(caret) namespace load failed Object sigma not found caret , . [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Choose Yes. 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. Open Source Biology & Genetics Interest Group. (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 . [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 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. I just figured Id ask. I even tried BiocManager::install("XML") but all failed as shown below. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Is the God of a monotheism necessarily omnipotent? Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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 When an R package depends on a newer package version, the required package is downloaded but not loaded. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. package rlang was built under R version 3.5.1. 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 mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running). What is a word for the arcane equivalent of a monastery? This includes any installed libraries. Loading required package: GenomeInfoDb [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Why is there a voltage on my HDMI and coaxial cables? One solution is to find all available packages. :), BiocManager::install("locift") To add to this, I have also been using DESeq2 recently and ran into the same problem. How to use Slater Type Orbitals as a basis functions in matrix method correctly? locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 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. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Is there a proper earth ground point in this switch box? install.packages("BiocManager"), I get this error: ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: How do you ensure that a red herring doesn't violate Chekhov's gun? [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 [7] edgeR_3.16.5 limma_3.30.12 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. Bad: conda install -c bioconda bioconductor-deseq2. 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. . 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 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 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. ERROR: dependency Hmisc is not available for package DESeq2 [7] datasets methods base, other attached packages: I tried again and again was met with missing packages BUT!!! Any suggestions would be greatly appreciated. Acidity of alcohols and basicity of amines. If you preorder a special airline meal (e.g. Language(R, Python, SQL) I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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 . Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in From the console install.packages ("rlang") should fix this. I would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package. Sounds like you might have an issue with which R Rstudio is running. I tried following the instructions for 2019.7 as well and I am getting the same error. [1] stats4 parallel stats graphics grDevices utils You are doing something very wrong when installing your packages. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. 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: Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Try installing zip, and then loading olsrr. Disconnect between goals and daily tasksIs it me, or the industry? 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. 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. .onLoad failed in loadNamespace() for 'rlang', details: Installing package(s) 'htmlTable', 'xfun' Warning message: Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Looking for incompatible packages.This can take several minutes. In addition: Warning message: How can we prove that the supernatural or paranormal doesn't exist? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, It is working now. Does a summoned creature play immediately after being summoned by a ready action? R version 3.6.3 (2020-02-29) there is no package called data.table [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Old packages: 'RcppArmadillo', 'survival' Please remember to confirm an answer once you've received one. Join us at CRISPR workshops in Koper, Slovenia in 2023. March 1, 2023, 7:31pm [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 vegan) just to try it, does this inconvenience the caterers and staff? New replies are no longer allowed. I do know that it works well in qiime2-2020.6. I guess that means we can finally close this issue. and then updating the packages that command indicates. 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'. privacy statement. I can download DESeq2 using, User Agreement and Privacy This can take several minutes. installation of package GenomeInfoDbData had non-zero exit status. When you load the package, you can observe this error. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Making statements based on opinion; back them up with references or personal experience. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 9. Making statements based on opinion; back them up with references or personal experience. Feedback Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? [13] ggplot23.3.0 car3.0-7 carData3.0-3 You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. [69] tidyselect_1.0.0. 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. 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. package in your R session. Are you sure the R you're running from the command line is installed through Anaconda as well? 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

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