How can I fix error with loading package in R ? | ResearchGate [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 This topic was automatically closed 21 days after the last reply. Old packages: 'RcppArmadillo', 'survival' Looking for incompatible packages. To add to this, I have also been using DESeq2 recently and ran into the same problem. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Is there a single-word adjective for "having exceptionally strong moral principles"? Policy. Error when installing Aldex2 - Community Plugin Support - Open Source 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). I just figured Id ask. Connect and share knowledge within a single location that is structured and easy to search. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. 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. So, supposedly the issue is with Hmisc. 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. running multiple versions of the same package, keeping separate libraries for some projects). [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 To resolve this error, install the required package as a cluster-installed library. [69] tidyselect_1.0.0. This article explains how to resolve the package or namespace loading error. there is no package called Hmisc. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [5] IRanges_2.8.1 S4Vectors_0.12.1 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. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Thanks for contributing an answer to Stack Overflow! By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. It only takes a minute to sign up. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Solution To resolve this error, install the required package as a cluster-installed library. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Why do many companies reject expired SSL certificates as bugs in bug bounties? "After the incident", I started to be more careful not to trip over things. [7] edgeR_3.16.5 limma_3.30.12 This includes any installed libraries. So if you still get this error try changing your CRAN mirror. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. rev2023.3.3.43278. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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. Install DESeq2 through anaconda - Bioinformatics Stack Exchange When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. [a/s/n]: Bioconductor - DESeq2 Press CTRL-C to abort. How to use Slater Type Orbitals as a basis functions in matrix method correctly? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 I highly recommend that any R/RStudio version not installed inside conda be removed. Did you do that? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. I was assuming that to be the case. Not the answer you're looking for? How can we prove that the supernatural or paranormal doesn't exist? Please try the following steps: Quit all R/Rstudio sessions. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? 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. DESeq2 installation in R - Bioconductor ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under More info about Internet Explorer and Microsoft Edge. I have tried your suggestion and also updating the packages that command indicates. Are there tables of wastage rates for different fruit and veg? Bioconductor release. Content type 'application/zip' length 233860 bytes (228 KB) [R] Error: package or namespace load failed for 'ggplot2' in After 3-4 manual installs everything worked. 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. DESeq2: Error: package or namespace load failed for 'DESeq2': objects rstudio - Error: package or namespace load failed for 'tidyverse Statistics ; Algorithm(ML, DL,.) While a notebook is attached to a cluster, the R namespace cannot be refreshed. Glad everything is finally working now. Is a PhD visitor considered as a visiting scholar? As such there are two solutions that may be more or less attainable given your own IT system. March 1, 2023, 4:56pm [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: to your account. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Platform: x86_64-apple-darwin17.0 (64-bit) sessionInfo() [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Convince your IT department to relax the permissions for R packages You signed in with another tab or window. Also make sure that you have RTools.exe installed and working. Looking for incompatible packages.This can take several minutes. I do know that it works well in qiime2-2020.6. Loading required package: GenomeInfoDb C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Please try reinstalling rlang on a fresh session. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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") Finally After 3-4 manual installations of missing packages everything worked. 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. When you load the package, you can observe this error. to allow custom library locations. 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 Running under: macOS Sierra 10.12.6. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Installing package(s) 'GenomeInfoDbData' (Factorization). BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Post questions about Bioconductor Use MathJax to format equations. 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. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Why is this sentence from The Great Gatsby grammatical? Use of this site constitutes acceptance of our User Agreement and Privacy package rlang was built under R version 3.5.1. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 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. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 To learn more, see our tips on writing great answers. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. ERROR: lazy loading failed for package Hmisc Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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). Policy. Is there anyone the same as mine error while loading library(DESeq2)? 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'. 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 library(DESeq2) Try again and choose No. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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. - the incident has nothing to do with me; can I use this this way? 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"). Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Acidity of alcohols and basicity of amines. No error messages are returned. If not fixed, Try removing remove.packages (rlang) then. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Warning message: To learn more, see our tips on writing great answers. - the incident has nothing to do with me; can I use this this way? I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 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'. How do I align things in the following tabular environment? nnet, spatial, survival. Should I update the Bioconductor to latest version instead? call: dots_list() biocLite(), install.packages() (and the devtools equivalent?) Error: package or namespace load failed for 'DESeq2 - Bioconductor 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. Is there a proper earth ground point in this switch box? 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. library (olsrr) - Error - General - RStudio Community I even tried BiocManager::install("XML") but all failed as shown below. Is a PhD visitor considered as a visiting scholar? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). ()library(DESeq2):Error in loadNamespace: no package called ""s Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) I also tried something I found on google: but the installation had errors too, I can write them here if needed. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked library(DESeq2) New replies are no longer allowed. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Bad: conda install -c bioconda bioconductor-deseq2. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. . 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 . "After the incident", I started to be more careful not to trip over things. To learn more, see our tips on writing great answers.