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Have a question about this project? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. 1. A place where magic is studied and practiced? to allow custom library locations. 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]]) : It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. R DESeq2 - locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) there is no package called GenomeInfoDbData I would like to install DESeq2 for DE analysis. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( March 1, 2023, 4:56pm there is no package called GenomeInfoDbData You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. library(caret) namespace load failed Object sigma not error: object 'rlang_dots_list' not found I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Use of this site constitutes acceptance of our User Agreement and Privacy a, There are binary versions available but the source versions are later: 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. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . March 1, 2023, 8:52pm Does anyone know why I'm getting the following message when I load tidyverse in a new session. As such there are two solutions that may be more or less attainable given your own IT system. there is no package called Hmisc. Try again and choose No. Platform: x86_64-apple-darwin15.6.0 (64-bit) Thank you @hharder. I need help installing a package "DESeq2" having - RStudio Community "htmlTable", "xfun" 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. 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. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Thanks for contributing an answer to Stack Overflow! Please remember to confirm an answer once you've received one. How to use Slater Type Orbitals as a basis functions in matrix method correctly? The other option is to download and older version of locfit from the package archive and install manually. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Should I update the Bioconductor to latest version instead? Press CTRL-C to abort. I then launched the R application (from the finder, not RStudio) and installed BiocManager. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Why do many companies reject expired SSL certificates as bugs in bug bounties? installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Glad everything is finally working now. Any suggestions would be greatly appreciated. R version 4.0.1 (2020-06-06) Use MathJax to format equations. Just to add on -- do you require an old version of Bioconductor for your current project? [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. May I know is there any other approach I can try? What am I doing wrong here in the PlotLegends specification? Just realize that I need to write the script "library("DESeq2")" before I proceed. Policy. Start R to confirm they are gone. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Looking for incompatible packages.This can take several minutes. Not the answer you're looking for? Let me confer with the team. [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: - 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. [1] stats4 parallel stats graphics grDevices utils Warning message: package in your R session. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Remember to always click on the red Show me the content on this page notice when navigating these older versions. 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. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Running. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 DESeq2 installation in R - Bioconductor 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. [7] datasets methods base, other attached packages: I tried again and again was met with missing packages BUT!!! Convince your IT department to relax the permissions for R packages (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 . [16] phyloseq1.30.0, loaded via a namespace (and not attached): Is it suspicious or odd to stand by the gate of a GA airport watching the planes? im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. 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. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") I guess that means we can finally close this issue. [5] IRanges_2.8.1 S4Vectors_0.12.1 Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. How can I fix error with loading package in R ? | ResearchGate LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 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: It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 I thought that working in a new environment would help, but it didnt. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 to your account. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub 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. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 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. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [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. Warning message: Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Loading required package: GenomeInfoDb [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Warning: cannot remove prior installation of package xfun Post questions about Bioconductor Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Platform: x86_64-apple-darwin13.4.0 (64-bit) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): :), BiocManager::install("locift") Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Is there anyone the same as mine error while loading library(DESeq2)? Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Find centralized, trusted content and collaborate around the technologies you use most. 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]]): 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. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR When an R package depends on a newer package version, the required package is downloaded but not loaded. 9. Policy. Citation (from within R, Surly Straggler vs. other types of steel frames. Making statements based on opinion; back them up with references or personal experience. How do I align things in the following tabular environment? From the console install.packages ("rlang") should fix this. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). I would recommend installing an older version of QIIME 2 for this plugin to work. Feedback So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. No error messages are returned. I just figured Id ask. 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. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Then I reinstalled R then Rstudio then RTools. I was assuming that to be the case. So, supposedly the issue is with Hmisc. Surly Straggler vs. other types of steel frames. Warning: restored xfun, The downloaded binary packages are in That plugin is has not been updated to work with later releases of QIIME 2. R version 3.6.3 (2020-02-29) [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Policy. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Use of this site constitutes acceptance of our User Agreement and Privacy 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. What is a word for the arcane equivalent of a monastery? 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'. Install DESeq2 through anaconda - Bioinformatics Stack Exchange "After the incident", I started to be more careful not to trip over things. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. I'm trying to reproduce your problem, so being as precise as possible is important. Just updated my previous R to 4.01 and now I cant load DESeq2. 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. 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? 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. Follow Up: struct sockaddr storage initialization by network format-string. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 DESeq2_2301_76497647-CSDN 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Also make sure that you have RTools.exe installed and working. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Are you sure the R you're running from the command line is installed through Anaconda as well? Looking for incompatible packages. ERROR: lazy loading failed for package Hmisc installation of package GenomeInfoDbData had non-zero exit status. In install.packages() : To subscribe to this RSS feed, copy and paste this URL into your RSS reader. + ), update = TRUE, ask = FALSE) Why are physically impossible and logically impossible concepts considered separate in terms of probability?