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

[13] ggplot23.3.0 car3.0-7 carData3.0-3 @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. Retrying with flexible solve.Solving environment: Found conflicts! It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. + ), update = TRUE, ask = FALSE) Is a PhD visitor considered as a visiting scholar? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. If you have a query related to it or one of the replies, start a new topic and refer back with a link. I guess that means we can finally close this issue. What is the output of. Running under: macOS Sierra 10.12.6. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Let me confer with the team. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. - the incident has nothing to do with me; can I use this this way? How can I fix error with loading package in R ? | ResearchGate DESeq2_2301_76497647-CSDN Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. I would like to install DESeq2 for DE analysis. Installing package(s) 'GenomeInfoDbData' [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () I tried to download the "locfit" package but I can't find it anywhere. now when I tried installing the missing packages they did install. vegan) just to try it, does this inconvenience the caterers and staff? Asking for help, clarification, or responding to other answers. Glad everything is finally working now. Warning message: LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open package rlang was built under R version 3.5.1. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. That plugin is has not been updated to work with later releases of QIIME 2. Thanks for your suggestion. The best answers are voted up and rise to the top, Not the answer you're looking for? [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. 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). Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: 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. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat [7] datasets methods base, other attached packages: Solution To resolve this error, install the required package as a cluster-installed library. 9. We've tried this - and can replicate this issue on a completely new install with no existing package installs. 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. enter citation("DESeq2")): To install this package, start R (version Language(R, Python, SQL) Error: package GenomeInfoDb could not be loaded. May be the version has problem How can I do ? [1] stats4 parallel stats graphics grDevices utils My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? It only takes a minute to sign up. 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. 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 it would be good to hear any speculation you have of how this might have happened). there is no package called Hmisc. Connect and share knowledge within a single location that is structured and easy to search. Citation (from within R, 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 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Loading required package: GenomicRanges Well occasionally send you account related emails. 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. Policy. Styling contours by colour and by line thickness in QGIS. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Installation instructions to use this Please remember to confirm an answer once you've received one. 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. 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 downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 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. Why do academics stay as adjuncts for years rather than move around? I tried following the instructions for 2019.7 as well and I am getting the same error. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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? Have you tried install.packages("locfit") ? "htmlTable", "xfun" The other option is to download and older version of locfit from the package archive and install manually. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 install.packages ("zip") Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? "4.2") and enter: For older versions of R, please refer to the appropriate Does a summoned creature play immediately after being summoned by a ready action? March 1, 2023, 8:52pm As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Then I reinstalled R then Rstudio then RTools. library (olsrr) - Error - General - RStudio Community 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. Hello, "After the incident", I started to be more careful not to trip over things. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 So if you still get this error try changing your CRAN mirror. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 How can we prove that the supernatural or paranormal doesn't exist? Content type 'application/zip' length 4255589 bytes (4.1 MB) install.packages("BiocManager"), I get this error: Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Can't Load R DESeq2 Library, Installed All Missing Packages and Still As such there are two solutions that may be more or less attainable given your own IT system. 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. I hope you can see something I can't see and help me solving this issue. To resolve this error, install the required package as a cluster-installed library. there is no package called GenomeInfoDbData Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 biocLite(), install.packages() (and the devtools equivalent?) 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"). [a/s/n]: 0 packages out-of-date; 2 packages too new, BiocManager::install(c( 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: After 3-4 manual installs everything worked. 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 Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 You are doing something very wrong when installing your packages. R DESeq2 - library(caret) namespace load failed Object sigma not Surly Straggler vs. other types of steel frames. library(caret) namespace load failed Object sigma not found caret , . Making statements based on opinion; back them up with references or personal experience. I would recommend installing an older version of QIIME 2 for this plugin to work. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 sessionInfo() Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. When an R package depends on a newer package version, the required package is downloaded but not loaded. I was assuming that to be the case. Documentation Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Not the answer you're looking for? library(DESeq2) Connect and share knowledge within a single location that is structured and easy to search. error: object 'rlang_dots_list' not found Thanks for contributing an answer to Bioinformatics Stack Exchange! Error when installing Aldex2 - Community Plugin Support - Open Source R version 3.6.3 (2020-02-29) How do you ensure that a red herring doesn't violate Chekhov's gun? Bad: conda install -c bioconda bioconductor-deseq2. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Then I reinstalled R then Rstudio then RTools. Policy. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Content type 'application/zip' length 233860 bytes (228 KB) 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. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. You signed in with another tab or window. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Why is there a voltage on my HDMI and coaxial cables? 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. Content type 'application/zip' length 386703 bytes (377 KB) :), BiocManager::install("locift") Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked 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: Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) there is no package called GenomeInfoDbData C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Thank you @hharder. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, So, supposedly the issue is with Hmisc. 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'. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 R version 4.0.1 (2020-06-06) [7] edgeR_3.16.5 limma_3.30.12 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 [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. privacy statement. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. 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: If you try loading the DEseq2 library now, that might work. Making statements based on opinion; back them up with references or personal experience. This topic was automatically closed 21 days after the last reply. ERROR: dependency Hmisc is not available for package DESeq2 [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( nnet, spatial, survival. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 to allow custom library locations. Is there anything I can do to speed it up? It is working now. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub If not fixed, Try removing remove.packages (rlang) then. 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. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Open Source Biology & Genetics Interest Group. 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!!! I have tried your suggestion and also updating the packages that command indicates. installation of package GenomeInfoDbData had non-zero exit status. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 2. I then launched the R application (from the finder, not RStudio) and installed BiocManager. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. R version 3.6.1 (2019-07-05) [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 I am running a new install of R (3.5.0) and RStudio (1.1.414). Connect and share knowledge within a single location that is structured and easy to search. How to notate a grace note at the start of a bar with lilypond? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Is the God of a monotheism necessarily omnipotent? One solution is to find all available packages. While a notebook is attached to a cluster, the R namespace cannot be refreshed. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Use of this site constitutes acceptance of our User Agreement and Privacy [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Learn more about Stack Overflow the company, and our products. To learn more, see our tips on writing great answers. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Platform: x86_64-apple-darwin13.4.0 (64-bit) Do I need a thermal expansion tank if I already have a pressure tank? 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. Try again and choose No. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: and then updating the packages that command indicates. Choose Yes. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Any other suggestion? 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. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. DESeq2 installation in R - Bioconductor To learn more, see our tips on writing great answers. Policy. Are you sure the R you're running from the command line is installed through Anaconda as well? library(DESeq2) Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I thought that working in a new environment would help, but it didnt. https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6: https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip', User Agreement and Privacy Also note, however, that the error you got has been associated in the past with mirror outages. 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 . 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]]) : [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Policy. 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. By clicking Sign up for GitHub, you agree to our terms of service and [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Is there a proper earth ground point in this switch box? Sounds like you might have an issue with which R Rstudio is running. Why do many companies reject expired SSL certificates as bugs in bug bounties? It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Is there anyone the same as mine error while loading library(DESeq2)? Installing Hmisc as suggested above did not solve the issue. Looking for incompatible packages. Loading required package: GenomeInfoDb trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Installing package(s) 'htmlTable', 'xfun' [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 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.