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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. Policy. library(caret) namespace load failed Object sigma not found caret , . I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Update all/some/none? The package has place the R version constraint. Why is there a voltage on my HDMI and coaxial cables? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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. 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. I can download DESeq2 using, User Agreement and Privacy I am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. .onLoad failed in loadNamespace() for 'rlang', details: Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. there is no package called GenomeInfoDbData R version 4.0.1 (2020-06-06) In file.copy(savedcopy, lib, recursive = TRUE) : [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 [7] datasets methods base, other attached packages: enter citation("DESeq2")): To install this package, start R (version By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Policy. Open Source Biology & Genetics Interest Group. May be the version has problem How can I do ? Replacing broken pins/legs on a DIP IC package. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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 I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Let me confer with the team. Thanks for contributing an answer to Bioinformatics Stack Exchange! Find centralized, trusted content and collaborate around the technologies you use most. Try installing zip, and then loading olsrr. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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 How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. if (!require("BiocManager", quietly = TRUE)) Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? I hope you can see something I can't see and help me solving this issue. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Traffic: 307 users visited in the last hour, I am new to all this! If you have a query related to it or one of the replies, start a new topic and refer back with a link. More info about Internet Explorer and Microsoft Edge. So if you still get this error try changing your CRAN mirror. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Platform: x86_64-apple-darwin15.6.0 (64-bit) To learn more, see our tips on writing great answers. [5] IRanges_2.8.1 S4Vectors_0.12.1 Is there a proper earth ground point in this switch box? Warning: cannot remove prior installation of package xfun Convince your IT department to relax the permissions for R packages C:\R\R-3.4.3\library). [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 [a/s/n]: 2. 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. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). now when I tried installing the missing packages they did install. Give up and run everything from the "permitted" library location (e.g. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: [69] tidyselect_1.0.0. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 What am I doing wrong here in the PlotLegends specification? 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 do I align things in the following tabular environment? 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"). I thought that working in a new environment would help, but it didnt. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 What is the output of. Looking for incompatible packages.This can take several minutes. If you try loading the DEseq2 library now, that might work. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so To view documentation for the version of this package installed Thanks for contributing an answer to Stack Overflow! A place where magic is studied and practiced? Fortunately I was able to solve it by doing things from several suggested solutions. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Making statements based on opinion; back them up with references or personal experience. Disconnect between goals and daily tasksIs it me, or the industry? I installed the package successfully with conda, but Rstudio is apparently does not know about it. How do you ensure that a red herring doesn't violate Chekhov's gun? [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. Learn more about Stack Overflow the company, and our products. [16] phyloseq1.30.0, loaded via a namespace (and not attached): Asking for help, clarification, or responding to other answers. Installing package(s) 'GenomeInfoDbData' Just realize that I need to write the script "library("DESeq2")" before I proceed. 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). Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Warning message: 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'. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): sessionInfo() Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? I do know that it works well in qiime2-2020.6. "htmlTable", "xfun" Thank you @hharder. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 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' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: 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. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 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. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in 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. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: The best answers are voted up and rise to the top, Not the answer you're looking for? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. This article explains how to resolve the package or namespace loading error. By clicking Sign up for GitHub, you agree to our terms of service and The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: install.packages("BiocManager"), I get this error: [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 @artembus Sounds like it was a ton of work! I was assuming that to be the case. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Sounds like there might be an issue with conda setup? If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Choose Yes. 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. binary source needs_compilation 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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]]) : Follow Up: struct sockaddr storage initialization by network format-string. 9. to allow custom library locations. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Why do many companies reject expired SSL certificates as bugs in bug bounties? nnet, spatial, survival. Connect and share knowledge within a single location that is structured and easy to search. 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). 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 . Well occasionally send you account related emails. Sounds like you might have an issue with which R Rstudio is running. To resolve this error, install the required package as a cluster-installed library. Just to add on -- do you require an old version of Bioconductor for your current project? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Use MathJax to format equations. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Whats the grammar of "For those whose stories they are"? LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Surly Straggler vs. other types of steel frames. Finally After 3-4 manual installations of missing packages everything worked. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Is there anything I can do to speed it up? 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. 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: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Please try reinstalling rlang on a fresh session. (Factorization). I would recommend installing an older version of QIIME 2 for this plugin to work. Running under: Windows 10 x64 (build 18362), locale: 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. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. No error messages are returned. Platform: x86_64-apple-darwin13.4.0 (64-bit) Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Loading required package: GenomeInfoDb 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. :), BiocManager::install("locift") And finally, install the problem packages, perhaps also DESeq2. I have tried your suggestion and also updating the packages that command indicates. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 When you load the package, you can observe this error. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. That plugin is has not been updated to work with later releases of QIIME 2. package rlang was built under R version 3.5.1. The other option is to download and older version of locfit from the package archive and install manually. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Find centralized, trusted content and collaborate around the technologies you use most. In addition: Warning message: Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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. Have you tried install.packages("locfit") ? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [7] edgeR_3.16.5 limma_3.30.12 there is no package called GenomeInfoDbData 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: I'm trying to reproduce your problem, so being as precise as possible is important. Use of this site constitutes acceptance of our User Agreement and Privacy Looking for incompatible packages. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. to your account. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. I tried to download the "locfit" package but I can't find it anywhere. 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. [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: Warning: restored xfun, The downloaded binary packages are in "After the incident", I started to be more careful not to trip over things. there is no package called data.table in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Solving environment: Found conflicts! Content type 'application/zip' length 233860 bytes (228 KB) Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) biocLite(), install.packages() (and the devtools equivalent?) downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 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. Thanks for your suggestion. Why do academics stay as adjuncts for years rather than move around? Statistics ; Algorithm(ML, DL,.) [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 library(DESeq2) Retrying with flexible solve.Solving environment: Found conflicts! so I would try to use BiocManager::install("XML"). [1] stats4 parallel stats graphics grDevices utils Also make sure that you have RTools.exe installed and working. Please read the posting Content type 'application/zip' length 4255589 bytes (4.1 MB) 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. Use of this site constitutes acceptance of our User Agreement and Privacy [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( To learn more, see our tips on writing great answers. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. 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. Making statements based on opinion; back them up with references or personal experience. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Documentation Connect and share knowledge within a single location that is structured and easy to search. data . Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) March 1, 2023, 4:56pm Should I update the Bioconductor to latest version instead? Use this. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. (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 . I even tried BiocManager::install("XML") but all failed as shown below. 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 Surly Straggler vs. other types of steel frames. in your system, start R and enter: Follow Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 [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. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. privacy statement. March 1, 2023, 7:31pm Policy. 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? The error states that the current version is 0.4.5 but 0.4.10 is required. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 rev2023.3.3.43278. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 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 Policy. 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. Running under: macOS Sierra 10.12.6. Use of this site constitutes acceptance of our User Agreement and Privacy there is no package called Hmisc. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Thanks! [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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. Already on GitHub? Styling contours by colour and by line thickness in QGIS. 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 Why are physically impossible and logically impossible concepts considered separate in terms of probability? rev2023.3.3.43278. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Not the answer you're looking for? Whats the grammar of "For those whose stories they are"? + "htmlTable", "xfun" Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 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!!! 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. 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.