When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. now when I tried installing the missing packages they did install. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Is a PhD visitor considered as a visiting scholar? Follow Up: struct sockaddr storage initialization by network format-string. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. When you load the package, you can observe this error. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? install.packages("BiocManager"), I get this error: [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 To add to this, I have also been using DESeq2 recently and ran into the same problem. there is no package called data.table [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 if (!require("BiocManager", quietly = TRUE)) [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 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]]) : Surly Straggler vs. other types of steel frames. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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). Not the answer you're looking for? Policy. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 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 . Also make sure that you have RTools.exe installed and working. To learn more, see our tips on writing great answers. This includes any installed libraries. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 "After the incident", I started to be more careful not to trip over things. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. 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. Have you tried install.packages("locfit") ? March 1, 2023, 7:31pm 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. Warning message: To learn more, see our tips on writing great answers. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Thanks for contributing an answer to Stack Overflow! /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages 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. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 vegan) just to try it, does this inconvenience the caterers and staff? Use MathJax to format equations. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): C:\R\R-3.4.3\library). call: dots_list() You signed in with another tab or window. I even tried BiocManager::install("XML") but all failed as shown below. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so sessionInfo() Open Source Biology & Genetics Interest Group. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Error when installing Aldex2 - Community Plugin Support - Open Source (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 . running multiple versions of the same package, keeping separate libraries for some projects). Rload failed - The best answers are voted up and rise to the top, Not the answer you're looking for? downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in 9. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Also note, however, that the error you got has been associated in the past with mirror outages. March 1, 2023, 8:52pm 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'. Disconnect between goals and daily tasksIs it me, or the industry? Making statements based on opinion; back them up with references or personal experience. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Statistics ; Algorithm(ML, DL,.) Policy. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Resolving package or namespace loading error And finally, install the problem packages, perhaps also DESeq2. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Use of this site constitutes acceptance of our User Agreement and Privacy rev2023.3.3.43278. Connect and share knowledge within a single location that is structured and easy to search. I hope you can see something I can't see and help me solving this issue. Surly Straggler vs. other types of steel frames. 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. [69] tidyselect_1.0.0. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. library(caret) namespace load failed Object sigma not found caret , . /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Should I update the Bioconductor to latest version instead? R version 3.6.1 (2019-07-05) Running. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. A place where magic is studied and practiced? [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 I would recommend installing an older version of QIIME 2 for this plugin to work. 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"). [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 R| - Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Please remember to confirm an answer once you've received one. 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"). [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. I then launched the R application (from the finder, not RStudio) and installed BiocManager. If not fixed, Try removing remove.packages (rlang) then. Error: package or namespace load failed for 'DESeq2 - Bioconductor 1. I tried following the instructions for 2019.7 as well and I am getting the same error. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in New replies are no longer allowed. As such there are two solutions that may be more or less attainable given your own IT system. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? But I guess you have many problems with your installation, and I'd suggest. I guess that means we can finally close this issue. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) privacy statement. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Following successful installation of backports BiocManager::install ("DESeq2") will succeed under 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 Why are physically impossible and logically impossible concepts considered separate in terms of probability? Loading required package: GenomicRanges ERROR: lazy loading failed for package Hmisc How to use Slater Type Orbitals as a basis functions in matrix method correctly? If it fails, required operating system facilities are missing. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Let me confer with the team. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Sign in Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [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. 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 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Convince your IT department to relax the permissions for R packages trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' From the console install.packages ("rlang") should fix this. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? enter citation("DESeq2")): To install this package, start R (version I also tried something I found on google: but the installation had errors too, I can write them here if needed. Update all/some/none? [13] ggplot23.3.0 car3.0-7 carData3.0-3 May I know is there any other approach I can try? rev2023.3.3.43278. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. In install.packages() : If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Is the God of a monotheism necessarily omnipotent? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. I installed the package successfully with conda, but Rstudio is apparently does not know about it. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Traffic: 307 users visited in the last hour, I am new to all this! How do you ensure that a red herring doesn't violate Chekhov's gun? Erasmus+ funds available! Fortunately I was able to solve it by doing things from several suggested solutions. Policy. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: 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. and then updating the packages that command indicates. I would like to install DESeq2 for DE analysis. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open Can't Load R DESeq2 Library, Installed All Missing Packages and Still It only takes a minute to sign up. 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. Solution To resolve this error, install the required package as a cluster-installed library. Language(R, Python, SQL) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Then I reinstalled R then Rstudio then RTools. to allow custom library locations. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Any other suggestion? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Start R to confirm they are gone. Does a summoned creature play immediately after being summoned by a ready action? Is a PhD visitor considered as a visiting scholar? Glad everything is finally working now. Finally After 3-4 manual installations of missing packages everything worked. Just updated my previous R to 4.01 and now I cant load DESeq2. Whats the grammar of "For those whose stories they are"? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): rstudio - Error: package or namespace load failed for 'tidyverse [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. If you have a query related to it or one of the replies, start a new topic and refer back with a link. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) How do I align things in the following tabular environment? [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Policy. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 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. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Why do academics stay as adjuncts for years rather than move around? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. - the incident has nothing to do with me; can I use this this way? Is there a proper earth ground point in this switch box? March 1, 2023, 3:25pm In addition: Warning message: 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. Content type 'application/zip' length 386703 bytes (377 KB) Asking for help, clarification, or responding to other answers. To view documentation for the version of this package installed 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. error: object 'rlang_dots_list' not found 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.