Why do academics stay as adjuncts for years rather than move around? package rlang was built under R version 3.5.1. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Press CTRL-C to abort. [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: Installing Hmisc as suggested above did not solve the issue. If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. By clicking Sign up for GitHub, you agree to our terms of service and Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. 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. 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. C:\R\R-3.4.3\library). But I guess you have many problems with your installation, and I'd suggest. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Policy. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 (Factorization). Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? R DESeq2 - [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 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. Statistics ; Algorithm(ML, DL,.) 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) Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 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. I tried again and again was met with missing packages BUT!!! 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. In addition: Warning message: New replies are no longer allowed. As such there are two solutions that may be more or less attainable given your own IT system. Already on GitHub? [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Running under: Windows 10 x64 (build 18362), locale: Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. And finally, install the problem packages, perhaps also DESeq2. to your account. rev2023.3.3.43278. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? I just figured Id ask. library(caret) namespace load failed Object sigma not If you try loading the DEseq2 library now, that might work. Not the answer you're looking for? Use this. Citation (from within R, 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 in your system, start R and enter: Follow To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [7] datasets methods base, other attached packages: Making statements based on opinion; back them up with references or personal experience. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Please try the following steps: Quit all R/Rstudio sessions. @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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Update all/some/none? When an R package depends on a newer package version, the required package is downloaded but not loaded. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Is a PhD visitor considered as a visiting scholar? So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. 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. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 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. To view documentation for the version of this package installed Surly Straggler vs. other types of steel frames. installation of package GenomeInfoDbData had non-zero exit status. so I would try to use BiocManager::install("XML"). 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") Then I reinstalled R then Rstudio then RTools. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Language(R, Python, SQL) 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, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 The error states that the current version is 0.4.5 but 0.4.10 is required. 9. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): You are doing something very wrong when installing your packages. Open Source Biology & Genetics Interest Group. Well occasionally send you account related emails. 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: DESeq2 - I can't get the library to load - Bioconductor 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: From the console install.packages ("rlang") should fix this. A place where magic is studied and practiced? Disconnect between goals and daily tasksIs it me, or the industry? (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 . /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, In install.packages() : What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Learn more about Stack Overflow the company, and our products. binary source needs_compilation Please read the posting Making statements based on opinion; back them up with references or personal experience. 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. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' data . installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? rstudio - Error: package or namespace load failed for 'tidyverse [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Documentation Thanks! 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. Post questions about Bioconductor 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? Replacing broken pins/legs on a DIP IC package. Why is this sentence from The Great Gatsby grammatical? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Bioconductor release. 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"). running multiple versions of the same package, keeping separate libraries for some projects). Thanks for your suggestion. 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. R version 3.6.1 (2019-07-05) there is no package called Hmisc. Why are physically impossible and logically impossible concepts considered separate in terms of probability? Finally After 3-4 manual installations of missing packages everything worked. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open No error messages are returned. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. R| - [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Sounds like there might be an issue with conda setup? now when I tried installing the missing packages they did install. 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 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]]): [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. 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. 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!!! [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Connect and share knowledge within a single location that is structured and easy to search. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? biocLite(), install.packages() (and the devtools equivalent?) If not fixed, Try removing remove.packages (rlang) then. Follow Up: struct sockaddr storage initialization by network format-string. I even tried BiocManager::install("XML") but all failed as shown below. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) call: dots_list() [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 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. 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. error: object 'rlang_dots_list' not found [a/s/n]: downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Bioconductor - DESeq2 How to use Slater Type Orbitals as a basis functions in matrix method correctly? I hope you can see something I can't see and help me solving this issue. Traffic: 307 users visited in the last hour, I am new to all this! But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? To resolve this error, install the required package as a cluster-installed library. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. ERROR: lazy loading failed for package Hmisc Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Platform: x86_64-apple-darwin17.0 (64-bit) If you have a query related to it or one of the replies, start a new topic and refer back with a link. Use MathJax to format equations. May be the version has problem How can I do ? Content type 'application/zip' length 233860 bytes (228 KB) To subscribe to this RSS feed, copy and paste this URL into your RSS reader. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE What is the output of. Acidity of alcohols and basicity of amines. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Is there a proper earth ground point in this switch box? What is a word for the arcane equivalent of a monastery? Running. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Error: package or namespace load failed, object not found 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 @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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Start R to confirm they are gone. Connect and share knowledge within a single location that is structured and easy to search. R version 4.0.1 (2020-06-06) To learn more, see our tips on writing great answers. How do you ensure that a red herring doesn't violate Chekhov's gun? Running under: macOS Sierra 10.12.3, locale: Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: I then launched the R application (from the finder, not RStudio) and installed BiocManager. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Asking for help, clarification, or responding to other answers. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Just updated my previous R to 4.01 and now I cant load DESeq2. Join us at CRISPR workshops in Koper, Slovenia in 2023. Convince your IT department to relax the permissions for R packages [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 I need help installing a package "DESeq2" having - RStudio Community Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Please remember to confirm an answer once you've received one. To learn more, see our tips on writing great answers. Installing package(s) 'GenomeInfoDbData' 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? Thanks for contributing an answer to Stack Overflow! ERROR: dependency Hmisc is not available for package DESeq2 Resolving package or namespace loading error Find centralized, trusted content and collaborate around the technologies you use most. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR [16] phyloseq1.30.0, loaded via a namespace (and not attached): Is there anyone the same as mine error while loading library(DESeq2)? Should I update the Bioconductor to latest version instead? LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: 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'. 4. nnet, spatial, survival. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Loading required package: GenomeInfoDb You signed in with another tab or window. Platform: x86_64-apple-darwin15.6.0 (64-bit) 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"). R version 3.6.3 (2020-02-29) now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. This topic was automatically closed 21 days after the last reply. Thank you @hharder. One solution is to find all available packages. . - the incident has nothing to do with me; can I use this this way? 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: [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? 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. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. library(DESeq2) ()library(DESeq2):Error in loadNamespace: no package called ""s [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 I was assuming that to be the case. I guess that means we can finally close this issue. Not the answer you're looking for? [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 and then updating the packages that command indicates. Warning: restored xfun, The downloaded binary packages are in In file.copy(savedcopy, lib, recursive = TRUE) : enter citation("DESeq2")): To install this package, start R (version Just realize that I need to write the script "library("DESeq2")" before I proceed. 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. Do I need a thermal expansion tank if I already have a pressure tank? I can download DESeq2 using, User Agreement and Privacy there is no package called Hmisc. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Is a PhD visitor considered as a visiting scholar? 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 . library(caret) namespace load failed Object sigma not found caret , . downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in I'd take a look at need, to see if there are any insights to be had, so that you can correct the root problem rather than having to do this procedure with other packages. Thanks for contributing an answer to Bioinformatics Stack Exchange! Install DESeq2 through anaconda - Bioinformatics Stack Exchange 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). binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 Are there tables of wastage rates for different fruit and veg? 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 This includes any installed libraries. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!).