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[46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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. [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8, attached base packages: library(DESeq2) I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Are you sure the R you're running from the command line is installed through Anaconda as well? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Asking for help, clarification, or responding to other answers. 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. I just figured Id ask. 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. Running. In install.packages() : Just realize that I need to write the script "library("DESeq2")" before I proceed. I've copied the output below in case it helps with troubleshooting. install.packages("BiocManager"), I get this 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 . + "htmlTable", "xfun" I would like to install DESeq2 for DE analysis. Running under: macOS Sierra 10.12.3, locale: 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. 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. May I know is there any other approach I can try? 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: Give up and run everything from the "permitted" library location (e.g. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Please try reinstalling rlang on a fresh session. [13] ggplot23.3.0 car3.0-7 carData3.0-3 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. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 [1] stats4 parallel stats graphics grDevices utils Making statements based on opinion; back them up with references or personal experience. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Loading required package: GenomicRanges nnet, spatial, survival. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Warning: restored xfun, The downloaded binary packages are in It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 @artembus Sounds like it was a ton of work! Did you do that? Thanks for contributing an answer to Stack Overflow! Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Installing package(s) 'XML' So, supposedly the issue is with Hmisc. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. I highly recommend that any R/RStudio version not installed inside conda be removed. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. - the incident has nothing to do with me; can I use this this way? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Choose Yes. Use of this site constitutes acceptance of our User Agreement and Privacy I can download DESeq2 using, User Agreement and Privacy Solving environment: Found conflicts! [16] phyloseq1.30.0, loaded via a namespace (and not attached): Why are physically impossible and logically impossible concepts considered separate in terms of probability? [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( enter citation("DESeq2")): To install this package, start R (version @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. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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. @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. there is no package called GenomeInfoDbData If you try loading the DEseq2 library now, that might work. 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. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Platform: x86_64-apple-darwin13.4.0 (64-bit) Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext guide. Disconnect between goals and daily tasksIs it me, or the industry? 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'. rev2023.3.3.43278. 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. But I guess you have many problems with your installation, and I'd suggest. In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. Asking for help, clarification, or responding to other answers. 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. I do know that it works well in qiime2-2020.6. R version 4.0.1 (2020-06-06) Warning message: [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 And finally, install the problem packages, perhaps also DESeq2. Thanks for contributing an answer to Bioinformatics Stack Exchange! [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Open Source Biology & Genetics Interest Group. 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. Any other suggestion? March 1, 2023, 3:25pm call: dots_list() Is the God of a monotheism necessarily omnipotent? 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"). 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). downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [a/s/n]: 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. This can take several minutes. to your account. May be the version has problem How can I do ? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. .onLoad failed in loadNamespace() for 'rlang', details: 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!!! Policy. C:\R\R-3.4.3\library). [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. package rlang was built under R version 3.5.1. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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 The error states that the current version is 0.4.5 but 0.4.10 is required. - the incident has nothing to do with me; can I use this this way? To view documentation for the version of this package installed [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Any suggestions would be greatly appreciated. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 To add to this, I have also been using DESeq2 recently and ran into the same problem. How do you ensure that a red herring doesn't violate Chekhov's gun? downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Statistics ; Algorithm(ML, DL,.) nnet, spatial, survival Use MathJax to format equations. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 2. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. rev2023.3.3.43278. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). I'm trying to reproduce your problem, so being as precise as possible is important. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Making statements based on opinion; back them up with references or personal experience. Running under: macOS Sierra 10.12.6. The other option is to download and older version of locfit from the package archive and install manually. 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[53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Convince your IT department to relax the permissions for R packages Learn more about Stack Overflow the company, and our products. Let me confer with the team. Is a PhD visitor considered as a visiting scholar? By clicking Sign up for GitHub, you agree to our terms of service and Hello, Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Thank you @hharder. sessionInfo() rev2023.3.3.43278. New replies are no longer allowed. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Already on GitHub? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Sign in error: object 'rlang_dots_list' not found [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in When you load the package, you can observe this error. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' 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.