Running under: macOS Sierra 10.12.6. Use of this site constitutes acceptance of our User Agreement and Privacy Then I reinstalled R then Rstudio then RTools. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. It is working now. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. R version 3.6.3 (2020-02-29) Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Installing package(s) 'htmlTable', 'xfun' May I know is there any other approach I can try? Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages installation of package GenomeInfoDbData had non-zero exit status. package in your R session. 4. Error: package GenomeInfoDb could not be loaded. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. In addition: Warning message: 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. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. (Factorization). Please try the following steps: Quit all R/Rstudio sessions. To resolve this error, install the required package as a cluster-installed library. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in More info about Internet Explorer and Microsoft Edge. 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. [1] stats4 parallel stats graphics grDevices utils [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 To learn more, see our tips on writing great answers. Running under: macOS Sierra 10.12.3, locale: ERROR: dependency Hmisc is not available for package DESeq2 I've copied the output below in case it helps with troubleshooting. Documentation 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: After 3-4 manual installs everything worked. + ), update = TRUE, ask = FALSE) library(caret) namespace load failed Object sigma not found caret , . 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: 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). [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Replacing broken pins/legs on a DIP IC package. I'm having a similar error, but different package: library("DESeq2") I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Is a PhD visitor considered as a visiting scholar? install.packages("BiocManager"), I get this error: Do I need a thermal expansion tank if I already have a pressure tank? Why do many companies reject expired SSL certificates as bugs in bug bounties? Traffic: 307 users visited in the last hour, I am new to all this! library(DESeq2) Glad everything is finally working now. 1. I guess that means we can finally close this issue. Making statements based on opinion; back them up with references or personal experience. 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. Why do academics stay as adjuncts for years rather than move around? 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. vegan) just to try it, does this inconvenience the caterers and staff? @artembus Sounds like it was a ton of work! Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. While a notebook is attached to a cluster, the R namespace cannot be refreshed. [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: You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 I installed the package successfully with conda, but Rstudio is apparently does not know about it. Does a summoned creature play immediately after being summoned by a ready action? 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. If it fails, required operating system facilities are missing. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Platform: x86_64-apple-darwin15.6.0 (64-bit) [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 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. Join us at CRISPR workshops in Koper, Slovenia in 2023. binary source needs_compilation call: dots_list() rev2023.3.3.43278. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. By clicking Sign up for GitHub, you agree to our terms of service and Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so One solution is to find all available packages. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Surly Straggler vs. other types of steel frames. I tried to download the "locfit" package but I can't find it anywhere. Surly Straggler vs. other types of steel frames. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat if (!require("BiocManager", quietly = TRUE)) Solving environment: Found conflicts! Just to add on -- do you require an old version of Bioconductor for your current project? Looking for incompatible packages. 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. March 1, 2023, 8:52pm to your account. To learn more, see our tips on writing great answers. so I would try to use BiocManager::install("XML"). Thanks for contributing an answer to Bioinformatics Stack Exchange! install.packages ("zip") Retrying with flexible solve.Solving environment: Found conflicts! downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 there is no package called GenomeInfoDbData In install.packages() : "4.2") and enter: For older versions of R, please refer to the appropriate Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Use of this site constitutes acceptance of our User Agreement and Privacy 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. 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 now when I tried installing the missing packages they did install. I have tried your suggestion and also updating the packages that command indicates. Why do academics stay as adjuncts for years rather than move around? When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. This includes any installed libraries. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. rev2023.3.3.43278. I would like to install DESeq2 for DE analysis. Try again and choose No. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. We've tried this - and can replicate this issue on a completely new install with no existing package installs. I tried again and again was met with missing packages BUT!!! 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"). [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.
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