install.packages ("zip") 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. there is no package called Hmisc. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. library(DESeq2) 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). However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 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. 4. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. How to notate a grace note at the start of a bar with lilypond? [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Not the answer you're looking for? Installing package(s) 'htmlTable', 'xfun' Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. "4.2") and enter: For older versions of R, please refer to the appropriate Citation (from within R, enter citation ("DESeq2") ): Installation To install this package, start R (version "4.2") and enter: if (!require ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install ("DESeq2") For older versions of R, please refer to the appropriate Bioconductor release . Bad: conda install -c bioconda bioconductor-deseq2. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Warning: cannot remove prior installation of package xfun there is no package called GenomeInfoDbData Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Solution To resolve this error, install the required package as a cluster-installed library. Whats the grammar of "For those whose stories they are"? [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 a, There are binary versions available but the source versions are later: When an R package depends on a newer package version, the required package is downloaded but not loaded. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Feedback 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. I tried again and again was met with missing packages BUT!!! call: dots_list() To resolve this error, install the required package as a cluster-installed library. Running under: macOS Sierra 10.12.3, locale: March 1, 2023, 4:56pm Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) What is the output of. to allow custom library locations. When an R package depends on a newer package version, the required package is downloaded but not loaded. Policy. Error: package GenomeInfoDb could not be loaded. I tried following the instructions for 2019.7 as well and I am getting the same error. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( You are doing something very wrong when installing your packages. Does a summoned creature play immediately after being summoned by a ready action? there is no package called Hmisc. Are you sure the R you're running from the command line is installed through Anaconda as well? locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) In file.copy(savedcopy, lib, recursive = TRUE) : I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. This topic was automatically closed 21 days after the last reply. I would like to install DESeq2 for DE analysis. Surly Straggler vs. other types of steel frames. Why do many companies reject expired SSL certificates as bugs in bug bounties? "htmlTable", "xfun" I'm having a similar error, but different package: 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 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 [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. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. ERROR: dependency Hmisc is not available for package DESeq2 Making statements based on opinion; back them up with references or personal experience. Is there a proper earth ground point in this switch box? @Tung I've updated my R and RStudio versions (unfortunately I had to first convince my workplace to approve them) and installed the packages through R 3.5.1 however, I'm still getting the same rlang error. Any suggestions would be greatly appreciated. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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 [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 I also tried something I found on google: but the installation had errors too, I can write them here if needed. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. 2. I can download DESeq2 using, User Agreement and Privacy [5] IRanges_2.8.1 S4Vectors_0.12.1 Acidity of alcohols and basicity of amines. In addition: Warning message: More info about Internet Explorer and Microsoft Edge. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Replacing broken pins/legs on a DIP IC package. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? The error states that the current version is 0.4.5 but 0.4.10 is required. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Use this. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () nnet, spatial, survival After 3-4 manual installs everything worked. Please try the following steps: Quit all R/Rstudio sessions. 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"). Is there anything I can do to speed it up? If it fails, required operating system facilities are missing. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Policy. Also make sure that you have RTools.exe installed and working. error: object 'rlang_dots_list' not found check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. I do know that it works well in qiime2-2020.6. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 The other option is to download and older version of locfit from the package archive and install manually. Installing package(s) 'GenomeInfoDbData' Making statements based on opinion; back them up with references or personal experience. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. 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. How to use Slater Type Orbitals as a basis functions in matrix method correctly? I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [1] stats4 parallel stats graphics grDevices utils downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Thanks for contributing an answer to Stack Overflow! ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Did you do that? 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. Give up and run everything from the "permitted" library location (e.g. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. How do I align things in the following tabular environment? biocLite(), install.packages() (and the devtools equivalent?) I hope you can see something I can't see and help me solving this issue. MathJax reference. First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Sorry, I'm newbie. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Loading required package: GenomeInfoDb C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages enter citation("DESeq2")): To install this package, start R (version Platform: x86_64-apple-darwin15.6.0 (64-bit) [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Thanks! Citation (from within R, Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Solving environment: Found conflicts! Find centralized, trusted content and collaborate around the technologies you use most. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Thanks for your suggestion. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Is a PhD visitor considered as a visiting scholar? [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. library(caret) namespace load failed Object sigma not found caret , . 9. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. 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. Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. Thanks for contributing an answer to Bioinformatics Stack Exchange! Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, One solution is to find all available packages. Whats the grammar of "For those whose stories they are"? it would be good to hear any speculation you have of how this might have happened). Looking for incompatible packages. Have a question about this project? [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 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 Running under: Windows 10 x64 (build 18362), locale: Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Policy. So if you still get this error try changing your CRAN mirror. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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 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: 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 if (!require("BiocManager", quietly = TRUE)) Sign in 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. and then updating the packages that command indicates. 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. Installation instructions to use this [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Warning message: nnet, spatial, survival. The package has place the R version constraint. Traffic: 307 users visited in the last hour, I am new to all this! [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 I thought that working in a new environment would help, but it didnt. [7] datasets methods base, other attached packages: Language(R, Python, SQL) Also note, however, that the error you got has been associated in the past with mirror outages. R version 3.6.1 (2019-07-05) How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? guide. Hello, Why are physically impossible and logically impossible concepts considered separate in terms of probability? 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. Have you tried install.packages("locfit") ? LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 I'm trying to reproduce your problem, so being as precise as possible is important. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Styling contours by colour and by line thickness in QGIS. I highly recommend that any R/RStudio version not installed inside conda be removed. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 While a notebook is attached to a cluster, the R namespace cannot be refreshed. (I have the most recent version of tidyverse, RStudio, and R.) Error: package or namespace load failed for 'tidyverse': .onAttach failed in attachNamespace() for 'tidyverse', details: call: glue(str, .envir = .envir, .transformer = transformer . Following successful installation of backports BiocManager::install ("DESeq2") will succeed under + ), update = TRUE, ask = FALSE) Retrying with flexible solve.Solving environment: Found conflicts! 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 get a whole new environment and install an old version of Qiime but I still got a ton of conflicts and it didnt install. sessionInfo() [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 there is no package called data.table Open Source Biology & Genetics Interest Group. 1. Connect and share knowledge within a single location that is structured and easy to search. or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. Well occasionally send you account related emails. Connect and share knowledge within a single location that is structured and easy to search. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Erasmus+ funds available! Glad everything is finally working now. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so .onLoad failed in loadNamespace() for 'rlang', details: 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 vegan) just to try it, does this inconvenience the caterers and staff? [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 We've tried this - and can replicate this issue on a completely new install with no existing package installs. From the console install.packages ("rlang") should fix this. rev2023.3.3.43278. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Warning message: Old packages: 'RcppArmadillo', 'survival' Running. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 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. 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. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: privacy statement. It only takes a minute to sign up. To learn more, see our tips on writing great answers. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Policy. Press CTRL-C to abort. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Sounds like you might have an issue with which R Rstudio is running. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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. By clicking Sign up for GitHub, you agree to our terms of service and Just realize that I need to write the script "library("DESeq2")" before I proceed. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' When you load the package, you can observe this error. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Policy. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. (Factorization). survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in there is no package called GenomeInfoDbData Choose Yes. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. there is no package called locfit. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [a/s/n]: [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 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. I have tried your suggestion and also updating the packages that command indicates. How do you ensure that a red herring doesn't violate Chekhov's gun? rev2023.3.3.43278. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. This includes any installed libraries. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. [13] ggplot23.3.0 car3.0-7 carData3.0-3 As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. "After the incident", I started to be more careful not to trip over things. 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). The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I even tried BiocManager::install("XML") but all failed as shown below. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Why do academics stay as adjuncts for years rather than move around? 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. Platform: x86_64-apple-darwin17.0 (64-bit) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Any other suggestion? [7] edgeR_3.16.5 limma_3.30.12 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 binary source needs_compilation The best answers are voted up and rise to the top, Not the answer you're looking for? But I guess you have many problems with your installation, and I'd suggest. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Is a PhD visitor considered as a visiting scholar? [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Use of this site constitutes acceptance of our User Agreement and Privacy How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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. 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. That plugin is has not been updated to work with later releases of QIIME 2. sessionInfo() Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? March 1, 2023, 3:25pm [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Start R to confirm they are gone. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Please remember to confirm an answer once you've received one. No error messages are returned. . Remember to always click on the red Show me the content on this page notice when navigating these older versions. I would recommend installing an older version of QIIME 2 for this plugin to work. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 I installed the package successfully with conda, but Rstudio is apparently does not know about it. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()'