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/private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages 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'. Retrying with flexible solve.Solving environment: Found conflicts! Making statements based on opinion; back them up with references or personal experience. Sorry, I'm newbie. Looking for incompatible packages. How to notate a grace note at the start of a bar with lilypond? 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. [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: [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 What is the output of. library(DESeq2) I tried again and again was met with missing packages BUT!!! [1] stats4 parallel stats graphics grDevices utils I just figured Id ask. Warning: restored xfun, The downloaded binary packages are in [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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 'XML' so I would try to use BiocManager::install ("XML"). Post questions about Bioconductor Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Policy. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 If you try loading the DEseq2 library now, that might work. Thanks for contributing an answer to Stack Overflow! Do I need a thermal expansion tank if I already have a pressure tank? So, supposedly the issue is with Hmisc. (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 . Join us at CRISPR workshops in Koper, Slovenia in 2023. Warning message: call: dots_list() More info about Internet Explorer and Microsoft Edge. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat 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. Did you do that? Platform: x86_64-apple-darwin13.4.0 (64-bit) Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Should I update the Bioconductor to latest version instead? there is no package called GenomeInfoDbData Thanks for your suggestion. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) @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. By clicking Sign up for GitHub, you agree to our terms of service and Styling contours by colour and by line thickness in QGIS. Platform: x86_64-apple-darwin15.6.0 (64-bit) package in your R session. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Convince your IT department to relax the permissions for R packages Whats the grammar of "For those whose stories they are"? Installation instructions to use this I guess that means we can finally close this issue. This topic was automatically closed 21 days after the last reply. Is the God of a monotheism necessarily omnipotent? 2. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Installing package(s) 'GenomeInfoDbData' I hope you can see something I can't see and help me solving this issue. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. Use of this site constitutes acceptance of our User Agreement and Privacy [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 [7] datasets methods base, other attached packages: Policy. Making statements based on opinion; back them up with references or personal experience. In addition: Warning message: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. This includes any installed libraries. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 March 1, 2023, 4:56pm If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': + ), update = TRUE, ask = FALSE) Any suggestions would be greatly appreciated. May be the version has problem How can I do ? "4.2") and enter: For older versions of R, please refer to the appropriate Why is there a voltage on my HDMI and coaxial cables? Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. From the console install.packages ("rlang") should fix this. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. sessionInfo() Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. How to use Slater Type Orbitals as a basis functions in matrix method correctly? BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Fortunately I was able to solve it by doing things from several suggested solutions. How do I align things in the following tabular environment? You signed in with another tab or window. package rlang was built under R version 3.5.1. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 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. 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? check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. I then launched the R application (from the finder, not RStudio) and installed BiocManager. [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. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 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. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. 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. to allow custom library locations. Loading required package: GenomeInfoDb a, There are binary versions available but the source versions are later: How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. 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. This can take several minutes. You are doing something very wrong when installing your packages. so I would try to use BiocManager::install("XML"). I also tried something I found on google: but the installation had errors too, I can write them here if needed. Why are physically impossible and logically impossible concepts considered separate in terms of probability? there is no package called data.table [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [13] ggplot23.3.0 car3.0-7 carData3.0-3 Any other suggestion? MathJax reference. there is no package called Hmisc. When you load the package, you can observe this error. Is there anyone the same as mine error while loading library(DESeq2)? [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Erasmus+ funds available! C:\R\R-3.4.3\library). 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. Error: package GenomeInfoDb could not be loaded. 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: The other option is to download and older version of locfit from the package archive and install manually. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 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") 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. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Let me confer with the team. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. Please remember to confirm an answer once you've received one. Thanks! Does a summoned creature play immediately after being summoned by a ready action? .onLoad failed in loadNamespace() for 'rlang', details: [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Is it suspicious or odd to stand by the gate of a GA airport watching the planes? I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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. @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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): It is working now. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 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. March 1, 2023, 3:25pm Why is this sentence from The Great Gatsby grammatical? We've tried this - and can replicate this issue on a completely new install with no existing package installs. I thought that working in a new environment would help, but it didnt. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Already on GitHub? Please try reinstalling rlang on a fresh session. March 1, 2023, 8:52pm The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Running under: macOS Catalina 10.15.3, Matrix products: default Replacing broken pins/legs on a DIP IC package. install.packages ("zip") 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. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? 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 Traffic: 307 users visited in the last hour, I am new to all this! [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Why do academics stay as adjuncts for years rather than move around? How to use Slater Type Orbitals as a basis functions in matrix method correctly? [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Then I reinstalled R then Rstudio then RTools. Give up and run everything from the "permitted" library location (e.g. Are there tables of wastage rates for different fruit and veg? [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 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!!! + "htmlTable", "xfun" It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Running under: macOS Sierra 10.12.3, locale: Thank you @hharder. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. running multiple versions of the same package, keeping separate libraries for some projects). Hello, By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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). Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Start R to confirm they are gone. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Is a PhD visitor considered as a visiting scholar? To learn more, see our tips on writing great answers. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: When an R package depends on a newer package version, the required package is downloaded but not loaded. The error states that the current version is 0.4.5 but 0.4.10 is required. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? What is a word for the arcane equivalent of a monastery? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 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 . I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. I am running a new install of R (3.5.0) and RStudio (1.1.414). /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_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 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. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Solution To resolve this error, install the required package as a cluster-installed library. Find centralized, trusted content and collaborate around the technologies you use most. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Use MathJax to format equations. To learn more, see our tips on writing great answers. No error messages are returned. To resolve this error, install the required package as a cluster-installed library. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? I tried to download the "locfit" package but I can't find it anywhere. Use this. Is there a proper earth ground point in this switch box? New replies are no longer allowed. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Content type 'application/zip' length 233860 bytes (228 KB) If you have a query related to it or one of the replies, start a new topic and refer back with a link. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Also note, however, that the error you got has been associated in the past with mirror outages. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): now when I tried installing the missing packages they did install. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 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. 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 Whats the grammar of "For those whose stories they are"? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Open Source Biology & Genetics Interest Group. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. in your system, start R and enter: Follow in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Glad everything is finally working now. 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. there is no package called locfit. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE 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. I tried following the instructions for 2019.7 as well and I am getting the same error. [7] edgeR_3.16.5 limma_3.30.12 I'm having a similar error, but different package: library("DESeq2") Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 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 'locfit' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: Use of this site constitutes acceptance of our User Agreement and Privacy [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Solving environment: Found conflicts! 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. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Running under: Windows 10 x64 (build 18362), locale: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Just updated my previous R to 4.01 and now I cant load DESeq2. Loading required package: GenomicRanges [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 To add to this, I have also been using DESeq2 recently and ran into the same problem. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 9. Is there a single-word adjective for "having exceptionally strong moral principles"? The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths.

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