error: package or namespace load failed for 'deseq2

installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. it would be good to hear any speculation you have of how this might have happened). [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 One solution is to find all available packages. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): and then updating the packages that command indicates. I highly recommend that any R/RStudio version not installed inside conda be removed. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. 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. @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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. "htmlTable", "xfun" New replies are no longer allowed. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 + ), update = TRUE, ask = FALSE) Give up and run everything from the "permitted" library location (e.g. Not the answer you're looking for? Making statements based on opinion; back them up with references or personal experience. - the incident has nothing to do with me; can I use this this way? If you have a query related to it or one of the replies, start a new topic and refer back with a link. 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. Installing package(s) 'GenomeInfoDbData' Policy. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages To add to this, I have also been using DESeq2 recently and ran into the same problem. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Sounds like there might be an issue with conda setup? package xfun successfully unpacked and MD5 sums checked Did you do that? [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open Just updated my previous R to 4.01 and now I cant load DESeq2. Is a PhD visitor considered as a visiting scholar? 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 Does a summoned creature play immediately after being summoned by a ready action? Open Source Biology & Genetics Interest Group. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Warning message: What am I doing wrong here in the PlotLegends specification? When an R package depends on a newer package version, the required package is downloaded but not loaded. Should I update the Bioconductor to latest version instead? Follow Up: struct sockaddr storage initialization by network format-string. 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]]) : Is there a single-word adjective for "having exceptionally strong moral principles"? Why are physically impossible and logically impossible concepts considered separate in terms of probability? install.packages("BiocManager"), I get this error: 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. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Join us at CRISPR workshops in Koper, Slovenia in 2023. March 1, 2023, 3:25pm Already on GitHub? [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Glad everything is finally working now. 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. 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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? I thought that working in a new environment would help, but it didnt. 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). 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. I have tried your suggestion and also updating the packages that command indicates. Policy. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Is there a proper earth ground point in this switch box? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? :), BiocManager::install("locift") I tried following the instructions for 2019.7 as well and I am getting the same error. 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: [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 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. March 1, 2023, 4:56pm rev2023.3.3.43278. Any other suggestion? Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Have you tried install.packages("locfit") ? there is no package called Hmisc. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in If it fails, required operating system facilities are missing. I also tried something I found on google: but the installation had errors too, I can write them here if needed. Retrying with flexible solve.Solving environment: Found conflicts! Warning: restored xfun, The downloaded binary packages are in [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Bioconductor release. Sign in Thanks for contributing an answer to Bioinformatics Stack Exchange! Resolving package or namespace loading error Looking for incompatible 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'. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 [13] ggplot23.3.0 car3.0-7 carData3.0-3 [5] IRanges_2.8.1 S4Vectors_0.12.1 You signed in with another tab or window. Please try reinstalling rlang on a fresh session. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? rev2023.3.3.43278. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. 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. How do you ensure that a red herring doesn't violate Chekhov's gun? RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE What is the output of. Installing package(s) 'htmlTable', 'xfun' It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Asking for help, clarification, or responding to other answers. Hello, 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 After 3-4 manual installs everything worked. [7] edgeR_3.16.5 limma_3.30.12 Thanks for contributing an answer to Stack Overflow! Is there a proper earth ground point in this switch box? there is no package called locfit. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Installing Hmisc as suggested above did not solve the issue. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Solution To resolve this error, install the required package as a cluster-installed library. Asking for help, clarification, or responding to other answers. A place where magic is studied and practiced? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). "After the incident", I started to be more careful not to trip over things. library(DESeq2) I need help installing a package "DESeq2" having - RStudio Community Making statements based on opinion; back them up with references or personal experience. From the console install.packages ("rlang") should fix this. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Fortunately I was able to solve it by doing things from several suggested solutions. R version 3.6.3 (2020-02-29) May I know is there any other approach I can try? + "htmlTable", "xfun" Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Please remember to confirm an answer once you've received one. vegan) just to try it, does this inconvenience the caterers and staff? 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: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 a, There are binary versions available but the source versions are later: trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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. 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 But I guess you have many problems with your installation, and I'd suggest. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Post questions about Bioconductor Rload failed - DESeq2_2301_76497647-CSDN 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 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 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"). So, supposedly the issue is with Hmisc. This topic was automatically closed 21 days after the last reply. How can I fix error with loading package in R ? | ResearchGate check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Looking for incompatible packages.This can take several minutes. so I would try to use BiocManager::install("XML"). 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. Erasmus+ funds available! R version 4.0.1 (2020-06-06) Have a question about this project? I installed the package successfully with conda, but Rstudio is apparently does not know about it. 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. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. What is a word for the arcane equivalent of a monastery? Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 DESeq2 installation in R - Bioconductor [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Well occasionally send you account related emails. library(caret) namespace load failed Object sigma not found caret , . Replacing broken pins/legs on a DIP IC package. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. I would like to install DESeq2 for DE analysis. I've copied the output below in case it helps with troubleshooting. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Use MathJax to format equations. Acidity of alcohols and basicity of amines. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: running multiple versions of the same package, keeping separate libraries for some projects). [69] tidyselect_1.0.0. Thank you @hharder. 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"). ERROR: lazy loading failed for package Hmisc 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. You are doing something very wrong when installing your packages. In install.packages() : I'm having a similar error, but different package: library("DESeq2") privacy statement. Platform: x86_64-apple-darwin17.0 (64-bit) Why is there a voltage on my HDMI and coaxial cables? Are you sure the R you're running from the command line is installed through Anaconda as well? It is working now. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Thanks for contributing an answer to Stack Overflow! library(DESeq2) Language(R, Python, SQL) Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Citation (from within R, in your system, start R and enter: Follow Feedback Choose Yes. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Do I need a thermal expansion tank if I already have a pressure tank? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 I then launched the R application (from the finder, not RStudio) and installed BiocManager. If you try loading the DEseq2 library now, that might work. Why do academics stay as adjuncts for years rather than move around? When you load the package, you can observe this error. 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. Update all/some/none? 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!!! Old packages: 'RcppArmadillo', 'survival' 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. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib I was assuming that to be the case. Please try the following steps: Quit all R/Rstudio sessions. 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). downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? To learn more, see our tips on writing great answers. This article explains how to resolve the package or namespace loading error. Bioconductor - DESeq2 call: dots_list() [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 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. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Are there tables of wastage rates for different fruit and veg? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Platform: x86_64-apple-darwin13.4.0 (64-bit) Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Also note, however, that the error you got has been associated in the past with mirror outages. Warning: cannot remove prior installation of package xfun [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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. Traffic: 307 users visited in the last hour, I am new to all this! Error: package or namespace load failed for 'DESeq2 - Bioconductor 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 . Is there anyone the same as mine error while loading library(DESeq2)? The package has place the R version constraint. install.packages ("zip") Just realize that I need to write the script "library("DESeq2")" before I proceed. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. now when I tried installing the missing packages they did install. Thanks for your suggestion. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. rev2023.3.3.43278. 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 other option is to download and older version of locfit from the package archive and install manually. 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. @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. Why do academics stay as adjuncts for years rather than move around? Running under: macOS Sierra 10.12.3, locale: Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. R DESeq2 - Installing package(s) 'XML' [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 In addition: Warning message: Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Is a PhD visitor considered as a visiting scholar? installation of package GenomeInfoDbData had non-zero exit status. Running. How to notate a grace note at the start of a bar with lilypond? I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I am running a new install of R (3.5.0) and RStudio (1.1.414). Can't Load R DESeq2 Library, Installed All Missing Packages and Still I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. [16] phyloseq1.30.0, loaded via a namespace (and not attached): * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2.

Revere Police Most Wanted, Pericles' Funeral Oration Sparknotes, Scdc Classification Headquarters, Stephen Nolan Guests Tonight, Days Gone How To Change Camera Angle, Articles E