Thanks for contributing an answer to Stack Overflow! This article explains how to resolve the package or namespace loading error. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. In addition: Warning message: May I know is there any other approach I can try? RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () If it fails, required operating system facilities are missing. Then I reinstalled R then Rstudio then RTools. Please read the posting By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. sessionInfo() Try again and choose No. 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. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Citation (from within R, 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. Installing package(s) 'htmlTable', 'xfun' How to use Slater Type Orbitals as a basis functions in matrix method correctly? Policy. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. there is no package called GenomeInfoDbData In install.packages() : 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: a, There are binary versions available but the source versions are later: When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Retrying with flexible solve.Solving environment: Found conflicts! Installing package(s) 'GenomeInfoDbData' 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Making statements based on opinion; back them up with references or personal experience. And finally, install the problem packages, perhaps also DESeq2. I do know that it works well in qiime2-2020.6. 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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Why do academics stay as adjuncts for years rather than move around? Looking for incompatible packages. March 1, 2023, 7:31pm dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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. install.packages("BiocManager"), I get this error: Use MathJax to format equations. there is no package called Hmisc. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I tried installing DESeq2 using: but it run into a lot of errors (some missing packages for some dependency packages etc) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Use of this site constitutes acceptance of our User Agreement and Privacy To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I would like to install DESeq2 for DE analysis. To add to this, I have also been using DESeq2 recently and ran into the same problem. 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. Why do academics stay as adjuncts for years rather than move around? [1] stats4 parallel stats graphics grDevices utils Content type 'application/zip' length 386703 bytes (377 KB) /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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). Remember to always click on the red Show me the content on this page notice when navigating these older versions. As mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running). Installing package(s) 'XML' 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. installation of package GenomeInfoDbData had non-zero exit status. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages library(DESeq2) [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Running. Let me confer with the team. Feedback I've copied the output below in case it helps with troubleshooting. rev2023.3.3.43278. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' By clicking Sign up for GitHub, you agree to our terms of service and Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I also tried something I found on google: but the installation had errors too, I can write them here if needed. Not the answer you're looking for? Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 R version 3.6.3 (2020-02-29) To learn more, see our tips on writing great answers. 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 I tried again and again was met with missing packages BUT!!! package rlang was built under R version 3.5.1. I highly recommend that any R/RStudio version not installed inside conda be removed. To resolve this error, install the required package as a cluster-installed library. to allow custom library locations. Installation instructions to use this Policy. Why are physically impossible and logically impossible concepts considered separate in terms of probability? locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Convince your IT department to relax the permissions for R packages 2. If you try loading the DEseq2 library now, that might work. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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. 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"). there is no package called GenomeInfoDbData there is no package called Hmisc. May be the version has problem How can I do ? Also note, however, that the error you got has been associated in the past with mirror outages. biocLite(), install.packages() (and the devtools equivalent?) check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Why is this sentence from The Great Gatsby grammatical? Running under: Windows 10 x64 (build 18362), 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. Erasmus+ funds available! Asking for help, clarification, or responding to other answers. Policy. Warning: restored xfun, The downloaded binary packages are in Any other suggestion? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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. Statistics ; Algorithm(ML, DL,.) 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'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. Should I update the Bioconductor to latest version instead? im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. data . sessionInfo() Try installing zip, and then loading olsrr. 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 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. Old packages: 'RcppArmadillo', 'survival' What is the output of. Post questions about Bioconductor It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. 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. there is no package called data.table [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 I thought that working in a new environment would help, but it didnt. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Thanks! Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Why do many companies reject expired SSL certificates as bugs in bug bounties? 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. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 I even tried BiocManager::install("XML") but all failed as shown below. Well occasionally send you account related emails. .onLoad failed in loadNamespace() for 'rlang', details: [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: Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. 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'. [7] datasets methods base, other attached packages: It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Making statements based on opinion; back them up with references or personal experience. 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 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? 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"). 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. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [13] ggplot23.3.0 car3.0-7 carData3.0-3 [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Do I need a thermal expansion tank if I already have a pressure tank? The error states that the current version is 0.4.5 but 0.4.10 is required. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): How can we prove that the supernatural or paranormal doesn't exist? The other option is to download and older version of locfit from the package archive and install manually. Loading required package: GenomeInfoDb 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 was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? March 1, 2023, 8:52pm Is there a single-word adjective for "having exceptionally strong moral principles"? Start R to confirm they are gone. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. 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. so I would try to use BiocManager::install("XML"). You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. . Warning: cannot remove prior installation of package xfun (Factorization). The best answers are voted up and rise to the top, Not the answer you're looking for? 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: How do I align things in the following tabular environment? Also make sure that you have RTools.exe installed and working. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 library(caret) namespace load failed Object sigma not found caret , . Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R I would recommend installing an older version of QIIME 2 for this plugin to work. 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? now when I tried installing the missing packages they did install. vegan) just to try it, does this inconvenience the caterers and staff? Use this. Solving environment: Found conflicts! [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Fortunately I was able to solve it by doing things from several suggested solutions. 4. This includes any installed libraries. 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. Acidity of alcohols and basicity of amines. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 From the console install.packages ("rlang") should fix this. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. "4.2") and enter: For older versions of R, please refer to the appropriate Hello, By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Installing Hmisc as suggested above did not solve the issue. Policy. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Open Source Biology & Genetics Interest Group. Content type 'application/zip' length 4255589 bytes (4.1 MB) Connect and share knowledge within a single location that is structured and easy to search. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. package in your R session. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Press CTRL-C to abort. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Looking for incompatible packages.This can take several minutes. Is the God of a monotheism necessarily omnipotent? 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. Platform: x86_64-apple-darwin15.6.0 (64-bit) [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 To learn more, see our tips on writing great answers. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. call: dots_list() If you have a query related to it or one of the replies, start a new topic and refer back with a link. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. 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 [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): binary source needs_compilation New replies are no longer allowed. nnet, spatial, survival - the incident has nothing to do with me; can I use this this way? Replacing broken pins/legs on a DIP IC package. Did you do that? [16] phyloseq1.30.0, loaded via a namespace (and not attached): 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. Loading required package: GenomicRanges and then updating the packages that command indicates. 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. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: