error: package or namespace load failed for 'deseq2

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namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Warning message: You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. ERROR: dependency Hmisc is not available for package DESeq2 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. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Making statements based on opinion; back them up with references or personal experience. 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages March 1, 2023, 4:56pm Is a PhD visitor considered as a visiting scholar? To add to this, I have also been using DESeq2 recently and ran into the same problem. [7] datasets methods base, other attached packages: there is no package called GenomeInfoDbData Making statements based on opinion; back them up with references or personal experience. Convince your IT department to relax the permissions for R packages The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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. In file.copy(savedcopy, lib, recursive = TRUE) : I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Use this. to your account. R version 3.6.1 (2019-07-05) Running under: macOS Sierra 10.12.3, locale: You signed in with another tab or window. Running under: macOS Sierra 10.12.6. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. But I guess you have many problems with your installation, and I'd suggest. I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Policy. The error states that the current version is 0.4.5 but 0.4.10 is required. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Not the answer you're looking for? data . Sorry if I missed this, the question was quite long so I kind of skimmed, but I noticed that early on some of the packages were reported as requiring manual compilation from source. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Any other suggestion? Just realize that I need to write the script "library("DESeq2")" before I proceed. Please try reinstalling rlang on a fresh session. 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. Learn more about Stack Overflow the company, and our products. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): 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. Choose Yes. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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. Follow Up: struct sockaddr storage initialization by network format-string. 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. Are you sure the R you're running from the command line is installed through Anaconda as well? 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. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Post questions about Bioconductor [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Just to add on -- do you require an old version of Bioconductor for your current project? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Policy. It only takes a minute to sign up. Open Source Biology & Genetics Interest Group. Then I reinstalled R then Rstudio then RTools. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 The best answers are voted up and rise to the top, Not the answer you're looking for? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Not the answer you're looking for? library(DESeq2) 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. [7] edgeR_3.16.5 limma_3.30.12 Thanks for contributing an answer to Bioinformatics Stack Exchange! Is the God of a monotheism necessarily omnipotent? I tried to download the "locfit" package but I can't find it anywhere. 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. 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). 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. in your system, start R and enter: Follow I just figured Id ask. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 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 Installing package(s) 'htmlTable', 'xfun' But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () biocLite(), install.packages() (and the devtools equivalent?) [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 After 3-4 manual installs everything worked. Join us at CRISPR workshops in Koper, Slovenia in 2023. 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? 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. If you have a query related to it or one of the replies, start a new topic and refer back with a link. I would like to install DESeq2 for DE analysis. 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 I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. I highly recommend that any R/RStudio version not installed inside conda be removed. Connect and share knowledge within a single location that is structured and easy to search. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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"). How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Policy. Sorry, I'm newbie. Please read the posting [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 March 1, 2023, 3:25pm More info about Internet Explorer and Microsoft Edge. I can download DESeq2 using, User Agreement and Privacy Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 To resolve this error, install the required package as a cluster-installed library. 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. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 installation of package GenomeInfoDbData had non-zero exit status. Statistics ; Algorithm(ML, DL,.) 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. Sounds like there might be an issue with conda setup? What is the output of. @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. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, I also tried something I found on google: but the installation had errors too, I can write them here if needed. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. [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: Warning message: Bioconductor release. To learn more, see our tips on writing great answers. install.packages ("zip") Remember to always click on the red Show me the content on this page notice when navigating these older versions. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Disconnect between goals and daily tasksIs it me, or the industry? @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. Acidity of alcohols and basicity of amines. 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'. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . [5] IRanges_2.8.1 S4Vectors_0.12.1 [1] stats4 parallel stats graphics grDevices utils Is it suspicious or odd to stand by the gate of a GA airport watching the planes? If it fails, required operating system facilities are missing. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. [69] tidyselect_1.0.0. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Any suggestions would be greatly appreciated. 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 I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. @artembus Sounds like it was a ton of work! Retrying with flexible solve.Solving environment: Found conflicts! unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Why do academics stay as adjuncts for years rather than move around? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 I was assuming that to be the case. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Sounds like you might have an issue with which R Rstudio is running. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Is there anyone the same as mine error while loading library(DESeq2)? I have tried your suggestion and also updating the packages that command indicates. Platform: x86_64-apple-darwin17.0 (64-bit) 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. Looking for incompatible packages. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 I thought that working in a new environment would help, but it didnt. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Finally After 3-4 manual installations of missing packages everything worked. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Does a summoned creature play immediately after being summoned by a ready action? Fortunately I was able to solve it by doing things from several suggested solutions. (Factorization). Connect and share knowledge within a single location that is structured and easy to search. Documentation The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. You are doing something very wrong when installing your packages. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 How do I align things in the following tabular environment? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Use of this site constitutes acceptance of our User Agreement and Privacy [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Sign in 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. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE How to use Slater Type Orbitals as a basis functions in matrix method correctly? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. By clicking Sign up for GitHub, you agree to our terms of service and rev2023.3.3.43278. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Does anyone know why I'm getting the following message when I load tidyverse in a new session. "After the incident", I started to be more careful not to trip over things. R version 3.6.3 (2020-02-29) there is no package called locfit. :), BiocManager::install("locift") 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: 9. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages May I know is there any other approach I can try? [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang:

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