error: package or namespace load failed for 'deseq2

/private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Finally After 3-4 manual installations of missing packages everything worked. Please try reinstalling rlang on a fresh session. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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. I guess that means we can finally close this issue. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. Running under: macOS Sierra 10.12.6. 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. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Platform: x86_64-w64-mingw32/x64 (64-bit) Acidity of alcohols and basicity of amines. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat package in your R session. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. New replies are no longer allowed. Join us at CRISPR workshops in Koper, Slovenia in 2023. Is there anything I can do to speed it up? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. The best answers are voted up and rise to the top, Not the answer you're looking for? I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Making statements based on opinion; back them up with references or personal experience. Content type 'application/zip' length 386703 bytes (377 KB) Policy. binary source needs_compilation install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). C:\R\R-3.4.3\library). Erasmus+ funds available! While a notebook is attached to a cluster, the R namespace cannot be refreshed. Sounds like you might have an issue with which R Rstudio is running. 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: I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Then I reinstalled R then Rstudio then RTools. Citation (from within R, 4. Installing package(s) 'XML' * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. In addition: Warning message: [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Warning: cannot remove prior installation of package xfun I was assuming that to be the case. guide. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib running multiple versions of the same package, keeping separate libraries for some projects). [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. there is no package called GenomeInfoDbData What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Why do academics stay as adjuncts for years rather than move around? Connect and share knowledge within a single location that is structured and easy to search. 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 [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Use of this site constitutes acceptance of our User Agreement and Privacy im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Running. Statistics ; Algorithm(ML, DL,.) downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in R version 3.6.3 (2020-02-29) Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. It is working now. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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. 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. [13] ggplot23.3.0 car3.0-7 carData3.0-3 1. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat R version 3.6.1 (2019-07-05) (I have the most recent version of tidyverse, RStudio, and R.) Error: package or namespace load failed for 'tidyverse': .onAttach failed in attachNamespace() for 'tidyverse', details: call: glue(str, .envir = .envir, .transformer = transformer . 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. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. If you try loading the DEseq2 library now, that might work. to your account. Have a question about this project? there is no package called locfit. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. rev2023.3.3.43278. Thank you @hharder. 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. Use of this site constitutes acceptance of our User Agreement and Privacy Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): In file.copy(savedcopy, lib, recursive = TRUE) : I would recommend installing an older version of QIIME 2 for this plugin to work. @artembus Sounds like it was a ton of work! [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 How can we prove that the supernatural or paranormal doesn't exist? if (!require("BiocManager", quietly = TRUE)) Is there anyone the same as mine error while loading library(DESeq2)? Policy. Convince your IT department to relax the permissions for R packages Why is there a voltage on my HDMI and coaxial cables? library(DESeq2) Is there a proper earth ground point in this switch box? [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 How to notate a grace note at the start of a bar with lilypond? Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) From the console install.packages ("rlang") should fix this. March 1, 2023, 8:52pm in your system, start R and enter: Follow [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 I just figured Id ask. In install.packages() : nnet, spatial, survival [7] datasets methods base, other attached packages: You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Error: package GenomeInfoDb could not be loaded. @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. I also tried something I found on google: but the installation had errors too, I can write them here if needed. 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. Warning message: Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? What am I doing wrong here in the PlotLegends specification? Policy. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under 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. And finally, install the problem packages, perhaps also DESeq2. Start R to confirm they are gone. I'm having a similar error, but different package: library("DESeq2") Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Running under: macOS Catalina 10.15.3, Matrix products: default [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 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"). I then launched the R application (from the finder, not RStudio) and installed BiocManager. library(DESeq2) "4.2") and enter: For older versions of R, please refer to the appropriate Is there a single-word adjective for "having exceptionally strong moral principles"? Surly Straggler vs. other types of steel frames. .onLoad failed in loadNamespace() for 'rlang', details: error: object 'rlang_dots_list' not found now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. To resolve this error, install the required package as a cluster-installed library. Update all/some/none? This topic was automatically closed 21 days after the last reply. Sounds like there might be an issue with conda setup? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: You are doing something very wrong when installing your packages. I can download DESeq2 using, User Agreement and Privacy [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Well occasionally send you account related emails. Warning message: Policy. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. March 1, 2023, 7:31pm I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 rev2023.3.3.43278. Installing Hmisc as suggested above did not solve the issue. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: If it fails, required operating system facilities are missing. Platform: x86_64-apple-darwin17.0 (64-bit) check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 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. It only takes a minute to sign up. package xfun successfully unpacked and MD5 sums checked I tried following the instructions for 2019.7 as well and I am getting the same error. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, 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. 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]]) : problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied, BiocManager::install("XML") I installed the package successfully with conda, but Rstudio is apparently does not know about it. 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. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Please remember to confirm an answer once you've received one. R version 4.0.1 (2020-06-06) So if you still get this error try changing your CRAN mirror. Running under: Windows 10 x64 (build 18362), locale: I've copied the output below in case it helps with troubleshooting. To learn more, see our tips on writing great answers. data . Glad everything is finally working now. Also note, however, that the error you got has been associated in the past with mirror outages. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Fortunately I was able to solve it by doing things from several suggested solutions. package rlang was built under R version 3.5.1. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Connect and share knowledge within a single location that is structured and easy to search. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Asking for help, clarification, or responding to other answers. What is the output of. Please read the posting Post questions about Bioconductor 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 [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Find centralized, trusted content and collaborate around the technologies you use most. [7] edgeR_3.16.5 limma_3.30.12 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. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 there is no package called data.table 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: So, supposedly the issue is with Hmisc. install.packages("BiocManager"), I get this error: binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 Is a PhD visitor considered as a visiting scholar? :), BiocManager::install("locift") Loading required package: GenomeInfoDb so I would try to use BiocManager::install("XML"). To learn more, see our tips on writing great answers. Should I update the Bioconductor to latest version instead? ERROR: lazy loading failed for package Hmisc 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. it would be good to hear any speculation you have of how this might have happened). My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Use this. By clicking Sign up for GitHub, you agree to our terms of service and Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Thanks for your suggestion. Just realize that I need to write the script "library("DESeq2")" before I proceed. Installing package(s) 'GenomeInfoDbData' Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. I tried to download the "locfit" package but I can't find it anywhere. 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. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. "After the incident", I started to be more careful not to trip over things. Just to add on -- do you require an old version of Bioconductor for your current project? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. To add to this, I have also been using DESeq2 recently and ran into the same problem. Does a summoned creature play immediately after being summoned by a ready action? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) More info about Internet Explorer and Microsoft Edge. How to use Slater Type Orbitals as a basis functions in matrix method correctly? Use MathJax to format equations. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Try installing zip, and then loading olsrr. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source.

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