error: package or namespace load failed for 'deseq2

I'm having a similar error, but different package: library("DESeq2") Running under: Windows 10 x64 (build 18362), locale: Thanks for contributing an answer to Bioinformatics Stack Exchange! installation of package GenomeInfoDbData had non-zero exit status. [a/s/n]: Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Why is this sentence from The Great Gatsby grammatical? Surly Straggler vs. other types of steel frames. I need help installing a package "DESeq2" having - RStudio Community I would recommend installing an older version of QIIME 2 for this plugin to work. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Looking for incompatible packages.This can take several minutes. 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). However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Please try the following steps: Quit all R/Rstudio sessions. 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. Does a summoned creature play immediately after being summoned by a ready action? 2. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. Use of this site constitutes acceptance of our User Agreement and Privacy I installed the package successfully with conda, but Rstudio is apparently does not know about it. 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 [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 March 1, 2023, 4:56pm [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. The best answers are voted up and rise to the top, Not the answer you're looking for? Install DESeq2 through anaconda - Bioinformatics Stack Exchange library(caret) namespace load failed Object sigma not [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 rev2023.3.3.43278. Running under: macOS Sierra 10.12.6. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Styling contours by colour and by line thickness in QGIS. Statistics ; Algorithm(ML, DL,.) By clicking Sign up for GitHub, you agree to our terms of service and Solution To resolve this error, install the required package as a cluster-installed library. Error: package GenomeInfoDb could not be loaded. install.packages ("zip") @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. 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: How to notate a grace note at the start of a bar with lilypond? now when I tried installing the missing packages they did install. 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. Please try reinstalling rlang on a fresh session. Give up and run everything from the "permitted" library location (e.g. ERROR: dependency Hmisc is not available for package DESeq2 Why do many companies reject expired SSL certificates as bugs in bug bounties? - the incident has nothing to do with me; can I use this this way? I highly recommend that any R/RStudio version not installed inside conda be removed. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? The package has place the R version constraint. 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. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages - the incident has nothing to do with me; can I use this this way? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Try again and choose No. Why do academics stay as adjuncts for years rather than move around? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Installing Hmisc as suggested above did not solve the issue. 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!!! Join us at CRISPR workshops in Koper, Slovenia in 2023. Platform: x86_64-w64-mingw32/x64 (64-bit) I'm trying to reproduce your problem, so being as precise as possible is important. 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. binary source needs_compilation The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Already on GitHub? 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 there is no package called GenomeInfoDbData This includes any installed libraries. Just to add on -- do you require an old version of Bioconductor for your current project? Looking for incompatible packages. DESeq2 - I can't get the library to load - Bioconductor Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) I can download DESeq2 using, User Agreement and Privacy [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Documentation rev2023.3.3.43278. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) I then launched the R application (from the finder, not RStudio) and installed BiocManager. Also make sure that you have RTools.exe installed and working. Use of this site constitutes acceptance of our User Agreement and Privacy data . 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. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Running under: macOS Sierra 10.12.3, locale: Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc 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? Thank you @hharder. March 1, 2023, 8:52pm [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Sounds like you might have an issue with which R Rstudio is running. "After the incident", I started to be more careful not to trip over things. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Thanks for contributing an answer to Stack Overflow! Are there tables of wastage rates for different fruit and veg? This topic was automatically closed 21 days after the last reply. 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 xfun successfully unpacked and MD5 sums checked there is no package called locfit. Thanks! install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). If not fixed, Try removing remove.packages (rlang) then. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Follow Up: struct sockaddr storage initialization by network format-string. 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 Warning message: there is no package called GenomeInfoDbData Then I reinstalled R then Rstudio then RTools. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I guess that means we can finally close this issue. Platform: x86_64-apple-darwin15.6.0 (64-bit) there is no package called Hmisc. I also tried something I found on google: but the installation had errors too, I can write them here if needed. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. 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. Is there a single-word adjective for "having exceptionally strong moral principles"? When an R package depends on a newer package version, the required package is downloaded but not loaded. Whats the grammar of "For those whose stories they are"? [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Have a question about this project? 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. 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. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Not the answer you're looking for? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. library(DESeq2) [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [7] edgeR_3.16.5 limma_3.30.12 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Replacing broken pins/legs on a DIP IC package. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 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]]) : LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open [13] ggplot23.3.0 car3.0-7 carData3.0-3 A place where magic is studied and practiced? I have tried your suggestion and also updating the packages that command indicates. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. so I would try to use BiocManager::install("XML"). Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). a, There are binary versions available but the source versions are later: Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. 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. 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. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. New replies are no longer allowed. 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. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. library(caret) namespace load failed Object sigma not found caret , . 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 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. 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. Is a PhD visitor considered as a visiting scholar? Surly Straggler vs. other types of steel frames. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. package rlang was built under R version 3.5.1. 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. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Is there anyone the same as mine error while loading library(DESeq2)? ()library(DESeq2):Error in loadNamespace: no package called ""s Policy. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. But I guess you have many problems with your installation, and I'd suggest. The error states that the current version is 0.4.5 but 0.4.10 is required. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Open Source Biology & Genetics Interest Group. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Content type 'application/zip' length 386703 bytes (377 KB) Asking for help, clarification, or responding to other answers. [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: Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so In install.packages() : 0 packages out-of-date; 2 packages too new, BiocManager::install(c( How do you ensure that a red herring doesn't violate Chekhov's gun? Use this. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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. Hello, [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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). running multiple versions of the same package, keeping separate libraries for some projects). [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 it would be good to hear any speculation you have of how this might have happened). How to use Slater Type Orbitals as a basis functions in matrix method correctly? Not the answer you're looking for? unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Warning: cannot remove prior installation of package xfun From the console install.packages ("rlang") should fix this. Policy. (Factorization). Finally After 3-4 manual installations of missing packages everything worked. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. 4. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Loading required package: GenomeInfoDb I would like to install DESeq2 for DE analysis. 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. Did you do that? DESeq2 installation in R - Bioconductor Please read the posting Policy. March 1, 2023, 7:31pm C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [7] datasets methods base, other attached packages: Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? if (!require("BiocManager", quietly = TRUE)) I am running a new install of R (3.5.0) and RStudio (1.1.414). Error: package or namespace load failed for 'DESeq2 - Bioconductor call: dots_list() Making statements based on opinion; back them up with references or personal experience. "htmlTable", "xfun" Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 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 This can take several minutes. I thought that working in a new environment would help, but it didnt. Then I reinstalled R then Rstudio then RTools. @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. 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. error: object 'rlang_dots_list' not found [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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.

error: package or namespace load failed for 'deseq2 2023