downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked package rlang was built under R version 3.5.1. DESeq2_2301_76497647-CSDN Statistics ; Algorithm(ML, DL,.) library(DESeq2) Resolving package or namespace loading error 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 . Use MathJax to format equations. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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"). In addition: Warning message: there is no package called GenomeInfoDbData Running under: macOS Catalina 10.15.3, Matrix products: default vegan) just to try it, does this inconvenience the caterers and staff? [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Warning: restored xfun, The downloaded binary packages are in 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. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. if (!require("BiocManager", quietly = TRUE)) Thanks for contributing an answer to Stack Overflow! 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. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. enter citation("DESeq2")): To install this package, start R (version downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? now when I tried installing the missing packages they did install. Please read the posting Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) I am running a new install of R (3.5.0) and RStudio (1.1.414). Making statements based on opinion; back them up with references or personal experience. library(DESeq2) It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. This includes any installed libraries. Connect and share knowledge within a single location that is structured and easy to search. rev2023.3.3.43278. How can we prove that the supernatural or paranormal doesn't exist? 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. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Running. 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. I just figured Id ask. 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. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. rev2023.3.3.43278. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub So, supposedly the issue is with Hmisc. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Installing package(s) 'GenomeInfoDbData' [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 From the console install.packages ("rlang") should fix this. If not fixed, Try removing remove.packages (rlang) then. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 :), BiocManager::install("locift") 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 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Please try the following steps: Quit all R/Rstudio sessions. biocLite(), install.packages() (and the devtools equivalent?) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Erasmus+ funds available! there is no package called data.table nnet, spatial, survival. Loading required package: GenomeInfoDb Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, To learn more, see our tips on writing great answers. Error: package GenomeInfoDb could not be loaded. Use of this site constitutes acceptance of our User Agreement and Privacy Installing Hmisc as suggested above did not solve the issue. 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). What is the output of. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. More info about Internet Explorer and Microsoft Edge. We've tried this - and can replicate this issue on a completely new install with no existing package installs. [a/s/n]: [13] ggplot23.3.0 car3.0-7 carData3.0-3 check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. (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 . Asking for help, clarification, or responding to other answers. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' I also tried something I found on google: but the installation had errors too, I can write them here if needed. 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'. 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. The other option is to download and older version of locfit from the package archive and install manually. March 1, 2023, 4:56pm Then I reinstalled R then Rstudio then RTools. Sounds like you might have an issue with which R Rstudio is running. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Whats the grammar of "For those whose stories they are"? [R] Error: package or namespace load failed for 'ggplot2' in R| - Follow Up: struct sockaddr storage initialization by network format-string. - the incident has nothing to do with me; can I use this this way? This topic was automatically closed 21 days after the last reply. R version 3.6.1 (2019-07-05) I then launched the R application (from the finder, not RStudio) and installed BiocManager. Sorry, I'm newbie. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' To learn more, see our tips on writing great answers. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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). [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Are there tables of wastage rates for different fruit and veg? Running under: macOS Sierra 10.12.6. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Open Source Biology & Genetics Interest Group. It is working now. Content type 'application/zip' length 4255589 bytes (4.1 MB) 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. After 3-4 manual installs everything worked. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. What is a word for the arcane equivalent of a monastery? Policy. 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. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. Sounds like there might be an issue with conda setup? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) call: dots_list() Solving environment: Found conflicts! Also make sure that you have RTools.exe installed and working. Replacing broken pins/legs on a DIP IC package. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Why do academics stay as adjuncts for years rather than move around? I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. March 1, 2023, 8:52pm [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Let me confer with the team. [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.