error: package or namespace load failed for 'deseq2

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. install.packages ("zip") Whats the grammar of "For those whose stories they are"? 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. Follow Up: struct sockaddr storage initialization by network format-string. 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. Solving environment: Found conflicts! You signed in with another tab or window. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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]]): Is there anyone the same as mine error while loading library(DESeq2)? Installing package(s) 'XML' 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"). If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Finally After 3-4 manual installations of missing packages everything worked. Content type 'application/zip' length 233860 bytes (228 KB) Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Any suggestions would be greatly appreciated. When you load the package, you can observe this error. Styling contours by colour and by line thickness in QGIS. 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 As mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running). 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. 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 guide. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Making statements based on opinion; back them up with references or personal experience. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. 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. 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. 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. I tried again and again was met with missing packages BUT!!! This is the beauty of installing QIIME 2 via conda, you can have many different versions of QIIME 2 on your system at the same time and activate the version you want to use. 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. enter citation("DESeq2")): To install this package, start R (version trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' - the incident has nothing to do with me; can I use this this way? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat 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. 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. Replacing broken pins/legs on a DIP IC package. If it fails, required operating system facilities are missing. Well occasionally send you account related emails. [16] phyloseq1.30.0, loaded via a namespace (and not attached): ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: there is no package called Hmisc. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Thanks for contributing an answer to Stack Overflow! No error messages are returned. The other option is to download and older version of locfit from the package archive and install manually. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc It is working now. Remember to always click on the red Show me the content on this page notice when navigating these older versions. Policy. How to use Slater Type Orbitals as a basis functions in matrix method correctly? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 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 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 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Making statements based on opinion; back them up with references or personal experience. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 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. 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]]) : Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Hello, Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). vegan) just to try it, does this inconvenience the caterers and staff? it would be good to hear any speculation you have of how this might have happened). 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Feedback ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Policy. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Are you sure the R you're running from the command line is installed through Anaconda as well? 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: When an R package depends on a newer package version, the required package is downloaded but not loaded. Looking for incompatible packages. How can we prove that the supernatural or paranormal doesn't exist? Running. Platform: x86_64-apple-darwin13.4.0 (64-bit) RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Thanks for contributing an answer to Bioinformatics Stack Exchange! .onLoad failed in loadNamespace() for 'rlang', details: LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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). Any other suggestion? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Have a question about this project? March 1, 2023, 8:52pm package xfun successfully unpacked and MD5 sums checked I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). May I know is there any other approach I can try? library(caret) namespace load failed Object sigma not found caret , . [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Use of this site constitutes acceptance of our User Agreement and Privacy I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Then I reinstalled R then Rstudio then RTools. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Let me confer with the team. What is a word for the arcane equivalent of a monastery? "htmlTable", "xfun" [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. The error states that the current version is 0.4.5 but 0.4.10 is required. Surly Straggler vs. other types of steel frames. R version 4.0.1 (2020-06-06) Why is this sentence from The Great Gatsby grammatical? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? C:\R\R-3.4.3\library).

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