Try again and choose No. binary source needs_compilation - the incident has nothing to do with me; can I use this this way? [69] tidyselect_1.0.0. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R I also tried something I found on google: but the installation had errors too, I can write them here if needed. Asking for help, clarification, or responding to other answers. No error messages are returned. When an R package depends on a newer package version, the required package is downloaded but not loaded. I hope you can see something I can't see and help me solving this issue. After 3-4 manual installs everything worked. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Citation (from within R, Making statements based on opinion; back them up with references or personal experience. Documentation Connect and share knowledge within a single location that is structured and easy to search. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Find centralized, trusted content and collaborate around the technologies you use most. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. privacy statement. data . Erasmus+ funds available! My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Find centralized, trusted content and collaborate around the technologies you use most. Bad: conda install -c bioconda bioconductor-deseq2. Does anyone know why I'm getting the following message when I load tidyverse in a new session. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. So, supposedly the issue is with Hmisc. I'm having a similar error, but different package: library("DESeq2") I tried to download the "locfit" package but I can't find it anywhere. (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 . 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!!! 4. 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: Do I need a thermal expansion tank if I already have a pressure tank? library(caret) namespace load failed Object sigma not found caret , . Please try the following steps: Quit all R/Rstudio sessions. 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). March 1, 2023, 3:25pm I am running a new install of R (3.5.0) and RStudio (1.1.414). [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Use this. 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. Post questions about Bioconductor rev2023.3.3.43278. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Follow Up: struct sockaddr storage initialization by network format-string. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. How do you ensure that a red herring doesn't violate Chekhov's gun? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. If you have a query related to it or one of the replies, start a new topic and refer back with a link. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. there is no package called Hmisc. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Retrying with flexible solve.Solving environment: Found conflicts! RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Installing Hmisc as suggested above did not solve the issue. When you load the package, you can observe this error. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Sounds like you might have an issue with which R Rstudio is running. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, I was assuming that to be the case. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. 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. 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") 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. Start R to confirm they are gone. sessionInfo() Error: package or namespace load failed, object not found [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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'. I do know that it works well in qiime2-2020.6. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 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. 9. 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 Policy. 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'. now when I tried installing the missing packages they did install. ERROR: dependency Hmisc is not available for package DESeq2 Glad everything is finally working now. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. I tried following the instructions for 2019.7 as well and I am getting the same error. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [13] ggplot23.3.0 car3.0-7 carData3.0-3 Open Source Biology & Genetics Interest Group. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. Learn more about Stack Overflow the company, and our products. + "htmlTable", "xfun" Warning: cannot remove prior installation of package xfun now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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 [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( To learn more, see our tips on writing great answers. there is no package called data.table 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"). 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. - the incident has nothing to do with me; can I use this this way? It is working now. 2. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Use of this site constitutes acceptance of our User Agreement and Privacy To learn more, see our tips on writing great answers. I can download DESeq2 using, User Agreement and Privacy Please read the posting 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. Platform: x86_64-apple-darwin15.6.0 (64-bit) Try installing zip, and then loading olsrr. Also note, however, that the error you got has been associated in the past with mirror outages. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Why do academics stay as adjuncts for years rather than move around? 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 . [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 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"). package xfun successfully unpacked and MD5 sums checked Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Thank you @hharder. 1. Warning message: Is a PhD visitor considered as a visiting scholar? Error: package or namespace load failed for 'DESeq2 - Bioconductor 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. Platform: x86_64-w64-mingw32/x64 (64-bit) [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( R version 4.0.1 (2020-06-06) /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): More info about Internet Explorer and Microsoft Edge. Loading required package: GenomeInfoDb DESeq2_2301_76497647-CSDN Thanks for contributing an answer to Stack Overflow! Update all/some/none? However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Thanks for contributing an answer to Stack Overflow! By clicking Sign up for GitHub, you agree to our terms of service and How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. [R] Error: package or namespace load failed for 'ggplot2' in [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: In install.packages() : library(DESeq2) guide. library(caret) namespace load failed Object sigma not install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. rev2023.3.3.43278. If it fails, required operating system facilities are missing. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 error: object 'rlang_dots_list' not found [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). If you preorder a special airline meal (e.g. Solving environment: Found conflicts! Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Are you sure the R you're running from the command line is installed through Anaconda as well? 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 . Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Running under: macOS Sierra 10.12.3, locale: [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): there is no package called GenomeInfoDbData 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. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 It only takes a minute to sign up. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Content type 'application/zip' length 233860 bytes (228 KB) Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 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. Well occasionally send you account related emails. Installing package(s) 'XML' Running under: macOS Catalina 10.15.3, Matrix products: default 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [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: Is there a proper earth ground point in this switch box? I installed the package successfully with conda, but Rstudio is apparently does not know about it. [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: Fortunately I was able to solve it by doing things from several suggested solutions. Warning: restored xfun, The downloaded binary packages are in But I guess you have many problems with your installation, and I'd suggest. One solution is to find all available packages. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open I have tried your suggestion and also updating the packages that command indicates. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. While a notebook is attached to a cluster, the R namespace cannot be refreshed. What am I doing wrong here in the PlotLegends specification? Policy. Surly Straggler vs. other types of steel frames. + ), update = TRUE, ask = FALSE) Just realize that I need to write the script "library("DESeq2")" before I proceed. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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. 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 package has place the R version constraint. sessionInfo() so I would try to use BiocManager::install("XML"). CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. 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. Already on GitHub? I've copied the output below in case it helps with troubleshooting. DESeq2 - I can't get the library to load - Bioconductor Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) The error states that the current version is 0.4.5 but 0.4.10 is required. .onLoad failed in loadNamespace() for 'rlang', details: Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? March 1, 2023, 4:56pm As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 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 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Policy. Convince your IT department to relax the permissions for R packages Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. 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: in your system, start R and enter: Follow Is there anyone the same as mine error while loading library(DESeq2)? 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. This can take several minutes. Sign in Is there anything I can do to speed it up? 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. I just figured Id ask. How to use Slater Type Orbitals as a basis functions in matrix method correctly? * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Give up and run everything from the "permitted" library location (e.g. to your account. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 "htmlTable", "xfun" Press CTRL-C to abort. there is no package called GenomeInfoDbData [5] IRanges_2.8.1 S4Vectors_0.12.1 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. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR When you load the package, you can observe this error. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [1] stats4 parallel stats graphics grDevices utils 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. This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 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. Error: package GenomeInfoDb could not be loaded. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 We've tried this - and can replicate this issue on a completely new install with no existing package installs. [7] edgeR_3.16.5 limma_3.30.12 ERROR: lazy loading failed for package Hmisc biocLite(), install.packages() (and the devtools equivalent?) So if you still get this error try changing your CRAN mirror. Not the answer you're looking for? Statistics ; Algorithm(ML, DL,.) ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Platform: x86_64-apple-darwin13.4.0 (64-bit) Why is there a voltage on my HDMI and coaxial cables? [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 . Policy. 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.
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