error: package or namespace load failed for 'deseq2

[11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 When an R package depends on a newer package version, the required package is downloaded but not loaded. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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). By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 4. "4.2") and enter: For older versions of R, please refer to the appropriate 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. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Policy. To add to this, I have also been using DESeq2 recently and ran into the same problem. @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. [69] tidyselect_1.0.0. Well occasionally send you account related emails. 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. Connect and share knowledge within a single location that is structured and easy to search. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. March 1, 2023, 8:52pm 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. Styling contours by colour and by line thickness in QGIS. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Give up and run everything from the "permitted" library location (e.g. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. and then updating the packages that command indicates. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Please try reinstalling rlang on a fresh session. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 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. What do I need to do to reproduce your problem? :), BiocManager::install("locift") Are you sure the R you're running from the command line is installed through Anaconda as well? 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. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. What is the output of. Join us at CRISPR workshops in Koper, Slovenia in 2023. How to use Slater Type Orbitals as a basis functions in matrix method correctly? This includes any installed libraries. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) March 1, 2023, 7:31pm To resolve this error, install the required package as a cluster-installed library. library(caret) namespace load failed Object sigma not found caret , . nnet, spatial, survival Why do academics stay as adjuncts for years rather than move around? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages The best answers are voted up and rise to the top, Not the answer you're looking for? Thanks for contributing an answer to Stack Overflow! Post questions about Bioconductor Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. 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. I have tried your suggestion and also updating the packages that command indicates. Already on GitHub? Are there tables of wastage rates for different fruit and veg? [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [5] IRanges_2.8.1 S4Vectors_0.12.1 [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 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. I would like to install DESeq2 for DE analysis. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Find centralized, trusted content and collaborate around the technologies you use most. Whats the grammar of "For those whose stories they are"? Traffic: 307 users visited in the last hour, I am new to all this! Solving environment: Found conflicts! 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. While a notebook is attached to a cluster, the R namespace cannot be refreshed. so I would try to use BiocManager::install("XML"). 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 I guess that means we can finally close this issue. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Policy. Use of this site constitutes acceptance of our User Agreement and Privacy Why do academics stay as adjuncts for years rather than move around? Running under: macOS Catalina 10.15.3, Matrix products: default "htmlTable", "xfun" 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. Then I reinstalled R then Rstudio then RTools. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Thank you @hharder. @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. Running. 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"). Choose Yes. a, There are binary versions available but the source versions are later: I tried following the instructions for 2019.7 as well and I am getting the same error. But I guess you have many problems with your installation, and I'd suggest. Does anyone know why I'm getting the following message when I load tidyverse in a new session. [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: Not the answer you're looking for? Solution To resolve this error, install the required package as a cluster-installed library. Loading required package: GenomeInfoDb install.packages ("zip") survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Installing package(s) 'htmlTable', 'xfun' Surly Straggler vs. other types of steel frames. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' How do you ensure that a red herring doesn't violate Chekhov's gun? Sorry, I'm newbie. I even tried BiocManager::install("XML") but all failed as shown below. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. library(DESeq2) RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. I tried to download the "locfit" package but I can't find it anywhere. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Thanks for contributing an answer to Bioinformatics Stack Exchange! in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so To subscribe to this RSS feed, copy and paste this URL into your RSS reader. "After the incident", I started to be more careful not to trip over things. Use of this site constitutes acceptance of our User Agreement and Privacy 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. Please remember to confirm an answer once you've received one. Follow Up: struct sockaddr storage initialization by network format-string. 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]]): Sign in 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. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). 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. 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. Also make sure that you have RTools.exe installed and working. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () By clicking Sign up for GitHub, you agree to our terms of service and Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Do I need a thermal expansion tank if I already have a pressure tank? If it fails, required operating system facilities are missing. Installing Hmisc as suggested above did not solve the issue. 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. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Should I update the Bioconductor to latest version instead? Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. You are doing something very wrong when installing your packages. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. now when I tried installing the missing packages they did install. Any other suggestion? Documentation Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Bad: conda install -c bioconda bioconductor-deseq2. Update all/some/none? [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Disconnect between goals and daily tasksIs it me, or the industry? Running under: Windows 10 x64 (build 18362), locale: privacy statement. @artembus Sounds like it was a ton of work! binary source needs_compilation Statistics ; Algorithm(ML, DL,.) 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. Find centralized, trusted content and collaborate around the technologies you use most. if (!require("BiocManager", quietly = TRUE)) Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Installation instructions to use this 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. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. The package has place the R version constraint. 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. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 R version 3.6.3 (2020-02-29) it would be good to hear any speculation you have of how this might have happened). Error: package GenomeInfoDb could not be loaded. package in your R session. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. I just figured Id ask. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Is a PhD visitor considered as a visiting scholar? [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Policy. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. In install.packages() : Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Thanks for your suggestion. 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. 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: Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Not the answer you're looking for? Try again and choose No. 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. Use of this site constitutes acceptance of our User Agreement and Privacy [13] ggplot23.3.0 car3.0-7 carData3.0-3 What am I doing wrong here in the PlotLegends specification? Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. there is no package called locfit. I'm trying to reproduce your problem, so being as precise as possible is important. How to notate a grace note at the start of a bar with lilypond? No error messages are returned. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Warning: cannot remove prior installation of package xfun 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 Making statements based on opinion; back them up with references or personal experience. Connect and share knowledge within a single location that is structured and easy to search. (Factorization). I do know that it works well in qiime2-2020.6. 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. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Content type 'application/zip' length 4255589 bytes (4.1 MB) Asking for help, clarification, or responding to other answers. When you load the package, you can observe this error. I'm having a similar error, but different package: library("DESeq2") Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Surly Straggler vs. other types of steel frames. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Looking for incompatible packages. Sounds like there might be an issue with conda setup? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in March 1, 2023, 3:25pm [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. This topic was automatically closed 21 days after the last reply. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 In file.copy(savedcopy, lib, recursive = TRUE) : 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. The error states that the current version is 0.4.5 but 0.4.10 is required. - 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. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under 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. 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. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Sounds like you might have an issue with which R Rstudio is running. 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. March 1, 2023, 4:56pm However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 error: object 'rlang_dots_list' not found Feedback rev2023.3.3.43278. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. + "htmlTable", "xfun" May be the version has problem How can I do ? 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'. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 . Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? + ), update = TRUE, ask = FALSE) Use MathJax to format equations. Installing package(s) 'GenomeInfoDbData' ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR 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"). [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages It is working now. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Retrying with flexible solve.Solving environment: Found conflicts! I thought that working in a new environment would help, but it didnt. 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"). [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 MathJax reference. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 When an R package depends on a newer package version, the required package is downloaded but not loaded. Just to add on -- do you require an old version of Bioconductor for your current project? It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. I've copied the output below in case it helps with troubleshooting. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy.

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