It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 there is no package called data.table 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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? library(DESeq2) 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. 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"). 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: [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. No error messages are returned. running multiple versions of the same package, keeping separate libraries for some projects). Installing package(s) 'htmlTable', 'xfun' Making statements based on opinion; back them up with references or personal experience. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Thanks for contributing an answer to Bioinformatics Stack Exchange! Learn more about Stack Overflow the company, and our products. ERROR: dependency Hmisc is not available for package DESeq2 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 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: Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Platform: x86_64-apple-darwin13.4.0 (64-bit) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [7] edgeR_3.16.5 limma_3.30.12 I highly recommend that any R/RStudio version not installed inside conda be removed. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? to allow custom library locations. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Any other suggestion? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. In file.copy(savedcopy, lib, recursive = TRUE) : Then I reinstalled R then Rstudio then RTools. 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc @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. After 3-4 manual installs everything worked. 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: installation of package GenomeInfoDbData had non-zero exit status. I do know that it works well in qiime2-2020.6. 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"). Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? (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 . 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. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 I tried to download the "locfit" package but I can't find it anywhere. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Loading required package: GenomeInfoDb Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Not the answer you're looking for? Please read the posting binary source needs_compilation Is there anyone the same as mine error while loading library(DESeq2)? 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 . Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, This can take several minutes. privacy statement. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Why is there a voltage on my HDMI and coaxial cables? Remember to always click on the red Show me the content on this page notice when navigating these older versions. And finally, install the problem packages, perhaps also DESeq2. New replies are no longer allowed. Use this. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat The other option is to download and older version of locfit from the package archive and install manually. I am running a new install of R (3.5.0) and RStudio (1.1.414). Looking for incompatible packages.This can take several minutes. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 library(DESeq2) Content type 'application/zip' length 4255589 bytes (4.1 MB) error: object 'rlang_dots_list' not found While a notebook is attached to a cluster, the R namespace cannot be refreshed. Asking for help, clarification, or responding to other answers. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Running under: macOS Sierra 10.12.6. + "htmlTable", "xfun" To learn more, see our tips on writing great answers. Sorry, I'm newbie. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 nnet, spatial, survival Surly Straggler vs. other types of steel frames. As such there are two solutions that may be more or less attainable given your own IT system. Replacing broken pins/legs on a DIP IC package. 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 Is there a single-word adjective for "having exceptionally strong moral principles"? Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Is the God of a monotheism necessarily omnipotent? @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. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': now when I tried installing the missing packages they did install. 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. 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. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 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") Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. library(caret) namespace load failed Object sigma not found caret , . Please try the following steps: Quit all R/Rstudio sessions. 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. 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. [5] IRanges_2.8.1 S4Vectors_0.12.1 Running under: macOS Sierra 10.12.3, locale: [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Why are physically impossible and logically impossible concepts considered separate in terms of probability? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Is a PhD visitor considered as a visiting scholar? Disconnect between goals and daily tasksIs it me, or the industry? Post questions about Bioconductor Connect and share knowledge within a single location that is structured and easy to search. Have a question about this project? biocLite(), install.packages() (and the devtools equivalent?) 1. Making statements based on opinion; back them up with references or personal experience. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. Use of this site constitutes acceptance of our User Agreement and Privacy Language(R, Python, SQL) Fortunately I was able to solve it by doing things from several suggested solutions. Making statements based on opinion; back them up with references or personal experience. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Connect and share knowledge within a single location that is structured and easy to search. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. This article explains how to resolve the package or namespace loading error. Please try reinstalling rlang on a fresh session. When you load the package, you can observe this error. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. I've previously written a blog post about this topic, and I can say from experience that installing R packages through conda can cause lots of headaches. and then updating the packages that command indicates. 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. 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). trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' I tried following the instructions for 2019.7 as well and I am getting the same error. Use of this site constitutes acceptance of our User Agreement and Privacy 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'. Well occasionally send you account related emails. I've copied the output below in case it helps with troubleshooting. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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!!! Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Did you do that? there is no package called Hmisc. 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. "After the incident", I started to be more careful not to trip over things. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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. MathJax reference. 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 incident has nothing to do with me; can I use this this way? But I guess you have many problems with your installation, and I'd suggest. 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'. Content type 'application/zip' length 386703 bytes (377 KB) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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]]) : Give up and run everything from the "permitted" library location (e.g. Glad everything is finally working now. March 1, 2023, 3:25pm Surly Straggler vs. other types of steel frames. Are there tables of wastage rates for different fruit and veg? now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Have you tried install.packages("locfit") ? Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Is a PhD visitor considered as a visiting scholar? What is a word for the arcane equivalent of a monastery? 4. 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. 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. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Author: Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd], Maintainer: Michael Love
error: package or namespace load failed for 'deseq2
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