Error: package GenomeInfoDb could not be loaded. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc but when I go to load the libraries I get this error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 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. Not the answer you're looking for? 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. I guess that means we can finally close this issue. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages What is a word for the arcane equivalent of a monastery? Erasmus+ funds available! I tried following the instructions for 2019.7 as well and I am getting the same error. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? How to use Slater Type Orbitals as a basis functions in matrix method correctly? I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. If it fails, required operating system facilities are missing. 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. library(DESeq2) [69] tidyselect_1.0.0. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Thanks for contributing an answer to Stack Overflow! Glad everything is finally working now. Why do academics stay as adjuncts for years rather than move around? This topic was automatically closed 21 days after the last reply. 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 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? Try installing zip, and then loading olsrr. Whats the grammar of "For those whose stories they are"? 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. Is there anyone the same as mine error while loading library(DESeq2)? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) To add to this, I have also been using DESeq2 recently and ran into the same problem. 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. (Factorization). [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): [7] datasets methods base, other attached packages: it would be good to hear any speculation you have of how this might have happened). Making statements based on opinion; back them up with references or personal experience. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Join us at CRISPR workshops in Koper, Slovenia in 2023. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Use this. 1. Did you do that? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Platform: x86_64-apple-darwin15.6.0 (64-bit) March 1, 2023, 7:31pm Sounds like you might have an issue with which R Rstudio is running. 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. Bad: conda install -c bioconda bioconductor-deseq2. 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. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. May I know is there any other approach I can try? [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 The package has place the R version constraint. - the incident has nothing to do with me; can I use this this way? [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Hello, Installing Hmisc as suggested above did not solve the issue. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Just realize that I need to write the script "library("DESeq2")" before I proceed. there is no package called locfit. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 How to use Slater Type Orbitals as a basis functions in matrix method correctly? Connect and share knowledge within a single location that is structured and easy to search. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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? Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 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. 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. Learn more about Stack Overflow the company, and our products. Platform: x86_64-apple-darwin13.4.0 (64-bit) Try again and choose No. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 + ), update = TRUE, ask = FALSE) Use MathJax to format equations. 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. installation of package GenomeInfoDbData had non-zero exit status. biocLite(), install.packages() (and the devtools equivalent?) New replies are no longer allowed. No error messages are returned. Are there tables of wastage rates for different fruit and veg? 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"). We've tried this - and can replicate this issue on a completely new install with no existing package installs. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. I have tried your suggestion and also updating the packages that command indicates. Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Disconnect between goals and daily tasksIs it me, or the industry? [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 To resolve this error, install the required package as a cluster-installed library. Please try reinstalling rlang on a fresh session. Then I reinstalled R then Rstudio then RTools. It is working now. 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. Convince your IT department to relax the permissions for R packages March 1, 2023, 8:52pm This article explains how to resolve the package or namespace loading error. Follow Up: struct sockaddr storage initialization by network format-string. library(caret) namespace load failed Object sigma not found caret , . nnet, spatial, survival. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Any suggestions would be greatly appreciated. Use of this site constitutes acceptance of our User Agreement and Privacy installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Looking for incompatible packages. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. 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. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. I even tried BiocManager::install("XML") but all failed as shown below. Traffic: 307 users visited in the last hour, I am new to all this! It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Old packages: 'RcppArmadillo', 'survival' I tried again and again was met with missing packages BUT!!! [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 I installed the package successfully with conda, but Rstudio is apparently does not know about it. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. In addition: Warning message: Thanks! Use of this site constitutes acceptance of our User Agreement and Privacy Why are physically impossible and logically impossible concepts considered separate in terms of probability? 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. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Please read the posting Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I also tried something I found on google: but the installation had errors too, I can write them here if needed. To learn more, see our tips on writing great answers. R version 4.0.1 (2020-06-06) [7] edgeR_3.16.5 limma_3.30.12 LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib rev2023.3.3.43278. Surly Straggler vs. other types of steel frames. By clicking Sign up for GitHub, you agree to our terms of service and 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'. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Retrying with flexible solve.Solving environment: Found conflicts! sessionInfo() 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. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Sign in im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. 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. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 But I guess you have many problems with your installation, and I'd suggest. May be the version has problem How can I do ? I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Thanks for your suggestion. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Finally After 3-4 manual installations of missing packages everything worked. install.packages("BiocManager"), I get this error: You are doing something very wrong when installing your 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 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [1] stats4 parallel stats graphics grDevices utils March 1, 2023, 4:56pm Let me confer with the team. Give up and run everything from the "permitted" library location (e.g. Post questions about Bioconductor 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. running multiple versions of the same package, keeping separate libraries for some projects). While a notebook is attached to a cluster, the R namespace cannot be refreshed. Use of this site constitutes acceptance of our User Agreement and Privacy I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Warning: restored xfun, The downloaded binary packages are in [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 to your account. The error states that the current version is 0.4.5 but 0.4.10 is required. Policy. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' install.packages('
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