/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages This can take several minutes. Whats the grammar of "For those whose stories they are"? [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( 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. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Traffic: 307 users visited in the last hour, I am new to all this! Thanks for contributing an answer to Stack Overflow! Policy. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Well occasionally send you account related emails. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 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. Disconnect between goals and daily tasksIs it me, or the industry? Not the answer you're looking for? unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': 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. Fortunately I was able to solve it by doing things from several suggested solutions. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib March 1, 2023, 4:56pm Are there tables of wastage rates for different fruit and veg? [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Then I reinstalled R then Rstudio then RTools. Already on GitHub? Is a PhD visitor considered as a visiting scholar? downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in From the console install.packages ("rlang") should fix this. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. 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]]): It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 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. + ), update = TRUE, ask = FALSE) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. How to use Slater Type Orbitals as a basis functions in matrix method correctly? I tried following the instructions for 2019.7 as well and I am getting the same error. Policy. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 nnet, spatial, survival I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Are you sure the R you're running from the command line is installed through Anaconda as well? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Warning: restored xfun, The downloaded binary packages are in New replies are no longer allowed. 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"). [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Sounds like you might have an issue with which R Rstudio is running. 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. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: To view documentation for the version of this package installed [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Connect and share knowledge within a single location that is structured and easy to search. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Loading required package: GenomicRanges Asking for help, clarification, or responding to other answers. "htmlTable", "xfun" @KonradRudolph It's pacman (not packman) and you are correct in that it's basically just a wrapper for, Thanks for your suggestion, I tried doing this step by step as you said but the biocLite command still did throw errors for missing packages. What is a word for the arcane equivalent of a monastery? Is there a proper earth ground point in this switch box? Find centralized, trusted content and collaborate around the technologies you use most. When you load the package, you can observe this error. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Citation (from within R, Use of this site constitutes acceptance of our User Agreement and Privacy Installation instructions to use this Hello, [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Thanks for contributing an answer to Bioinformatics Stack Exchange! C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages "4.2") and enter: For older versions of R, please refer to the appropriate Sorry, I'm newbie. Connect and share knowledge within a single location that is structured and easy to search. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. - the incident has nothing to do with me; can I use this this way? If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. I've copied the output below in case it helps with troubleshooting. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I tried again and again was met with missing packages BUT!!! In file.copy(savedcopy, lib, recursive = TRUE) : [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Press CTRL-C to abort. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) In addition: Warning message: now when I tried installing the missing packages they did install. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Why do academics stay as adjuncts for years rather than move around? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: 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. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. [5] IRanges_2.8.1 S4Vectors_0.12.1 @artembus Sounds like it was a ton of work! sessionInfo() Content type 'application/zip' length 386703 bytes (377 KB) [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Surly Straggler vs. other types of steel frames. The best answers are voted up and rise to the top, Not the answer you're looking for? How do I align things in the following tabular environment? Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R C:\R\R-3.4.3\library). [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Is the God of a monotheism necessarily omnipotent? I installed the package successfully with conda, but Rstudio is apparently does not know about it. - the incident has nothing to do with me; can I use this this way? I'm trying to reproduce your problem, so being as precise as possible is important. biocLite(), install.packages() (and the devtools equivalent?) Then I reinstalled R then Rstudio then RTools. rev2023.3.3.43278. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. there is no package called locfit. Thanks for your suggestion. "After the incident", I started to be more careful not to trip over things. Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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. Open Source Biology & Genetics Interest Group. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 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.