:), BiocManager::install("locift") downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Traffic: 307 users visited in the last hour, I am new to all this! /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. 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. How do I align things in the following tabular environment? locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) It is working now. I highly recommend that any R/RStudio version not installed inside conda be removed. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Sorry, I'm newbie. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Policy. 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. The package has place the R version constraint. Policy. Surly Straggler vs. other types of steel frames. I do know that it works well in qiime2-2020.6. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. [7] edgeR_3.16.5 limma_3.30.12 The error states that the current version is 0.4.5 but 0.4.10 is required. Citation (from within R, I would recommend installing an older version of QIIME 2 for this plugin to work. [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. Warning message: RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE The best answers are voted up and rise to the top, Not the answer you're looking for? Press CTRL-C to abort. That plugin is has not been updated to work with later releases of QIIME 2. "After the incident", I started to be more careful not to trip over things. March 1, 2023, 3:25pm Asking for help, clarification, or responding to other answers. Start R to confirm they are gone. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. 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. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 (Factorization). [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: R version 4.0.1 (2020-06-06) 4. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' 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'. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Connect and share knowledge within a single location that is structured and easy to search. 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. 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 /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. 9. 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). Loading required package: GenomeInfoDb I've copied the output below in case it helps with troubleshooting. 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. Is the God of a monotheism necessarily omnipotent? install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). "htmlTable", "xfun" R version 3.6.1 (2019-07-05) Looking for incompatible packages. Hello, Please try the following steps: Quit all R/Rstudio sessions. Retrying with flexible solve.Solving environment: Found conflicts! The other option is to download and older version of locfit from the package archive and install manually. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 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? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Surly Straggler vs. other types of steel frames. and then updating the packages that command indicates. 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 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. Erasmus+ funds available! Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 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. How to notate a grace note at the start of a bar with lilypond? [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 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: I tried to download the "locfit" package but I can't find it anywhere. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Did you do that? I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. package rlang was built under R version 3.5.1. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Should I update the Bioconductor to latest version instead? 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") Is a PhD visitor considered as a visiting scholar? there is no package called data.table Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Why do many companies reject expired SSL certificates as bugs in bug bounties? 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"). Looking for incompatible packages.This can take several minutes. Are you sure the R you're running from the command line is installed through Anaconda as well? [1] stats4 parallel stats graphics grDevices utils 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. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): there is no package called Hmisc. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Platform: x86_64-apple-darwin15.6.0 (64-bit) Whats the grammar of "For those whose stories they are"? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Connect and share knowledge within a single location that is structured and easy to search. What am I doing wrong here in the PlotLegends specification? 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. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Running under: Windows 10 x64 (build 18362), locale: [13] ggplot23.3.0 car3.0-7 carData3.0-3 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 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. Any suggestions would be greatly appreciated. a, There are binary versions available but the source versions are later: I was assuming that to be the case. When an R package depends on a newer package version, the required package is downloaded but not loaded. Warning: restored xfun, The downloaded binary packages are in library(DESeq2) Policy. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Installing package(s) 'htmlTable', 'xfun' BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Also note, however, that the error you got has been associated in the past with mirror outages. 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: it would be good to hear any speculation you have of how this might have happened). im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. 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. Thanks for your suggestion. 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.
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