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Warning message: 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 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. Warning: restored xfun, The downloaded binary packages are in 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 To learn more, see our tips on writing great answers. Platform: x86_64-apple-darwin13.4.0 (64-bit) 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). Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Platform: x86_64-apple-darwin15.6.0 (64-bit) Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 When you load the package, you can observe this error. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. I can download DESeq2 using, User Agreement and Privacy [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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( package rlang was built under R version 3.5.1. I tried to download the "locfit" package but I can't find it anywhere. This topic was automatically closed 21 days after the last reply. I then launched the R application (from the finder, not RStudio) and installed BiocManager. When you load the package, you can observe this error. Platform: x86_64-w64-mingw32/x64 (64-bit) [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Update all/some/none? Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) - the incident has nothing to do with me; can I use this this way? Is a PhD visitor considered as a visiting scholar? vegan) just to try it, does this inconvenience the caterers and staff? I would recommend installing an older version of QIIME 2 for this plugin to work. In file.copy(savedcopy, lib, recursive = TRUE) : What is a word for the arcane equivalent of a monastery? But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () 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. [69] tidyselect_1.0.0. Warning: cannot remove prior installation of package xfun library(DESeq2) Does anyone know why I'm getting the following message when I load tidyverse in a new session. If not fixed, Try removing remove.packages (rlang) then. [1] stats4 parallel stats graphics grDevices utils However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. in your system, start R and enter: Follow Installing Hmisc as suggested above did not solve the issue. [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: No error messages are returned. and then updating the packages that command indicates. Policy. Also make sure that you have RTools.exe installed and working. biocLite(), install.packages() (and the devtools equivalent?) Running under: macOS Catalina 10.15.3, Matrix products: default Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat @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. Surly Straggler vs. other types of steel frames. Content type 'application/zip' length 233860 bytes (228 KB) Are you sure the R you're running from the command line is installed through Anaconda as well? C:\R\R-3.4.3\library). Try again and choose No. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in privacy statement. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. [5] IRanges_2.8.1 S4Vectors_0.12.1 Acidity of alcohols and basicity of amines. Sign in 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: ()library(DESeq2):Error in loadNamespace: no package called ""s I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. it would be good to hear any speculation you have of how this might have happened). 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. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 How to use Slater Type Orbitals as a basis functions in matrix method correctly? I installed the package successfully with conda, but Rstudio is apparently does not know about it. Use of this site constitutes acceptance of our User Agreement and Privacy [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : We've tried this - and can replicate this issue on a completely new install with no existing package installs. Just to add on -- do you require an old version of Bioconductor for your current project? Is the God of a monotheism necessarily omnipotent? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). I would like to install DESeq2 for DE analysis. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Thanks for contributing an answer to Bioinformatics Stack Exchange! install.packages ("zip") requires R 4 and running more than a couple of releases behind in R risks multiplying problems. When an R package depends on a newer package version, the required package is downloaded but not loaded. Start R to confirm they are gone. Open Source Biology & Genetics Interest Group. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Choose Yes. 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. 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). You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Surly Straggler vs. other types of steel frames. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) You signed in with another tab or window. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Sounds like you might have an issue with which R Rstudio is running. Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. 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. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Let me confer with the team. 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. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? If you have a query related to it or one of the replies, start a new topic and refer back with a link. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Fortunately I was able to solve it by doing things from several suggested solutions. Why are physically impossible and logically impossible concepts considered separate in terms of probability? Content type 'application/zip' length 386703 bytes (377 KB) + ), update = TRUE, ask = FALSE) [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 rev2023.3.3.43278. The other option is to download and older version of locfit from the package archive and install manually. "4.2") and enter: For older versions of R, please refer to the appropriate I guess that means we can finally close this issue. What is the output of. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Following successful installation of backports BiocManager::install ("DESeq2") will succeed under March 1, 2023, 3:25pm there is no package called Hmisc. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 nnet, spatial, survival LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: I tried again and again was met with missing packages BUT!!! Is there a single-word adjective for "having exceptionally strong moral principles"? a, There are binary versions available but the source versions are later: 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. Making statements based on opinion; back them up with references or personal experience. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. 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. Asking for help, clarification, or responding to other answers. If you preorder a special airline meal (e.g. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Then I reinstalled R then Rstudio then RTools. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Policy. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Solving environment: Found conflicts! Loading required package: GenomeInfoDb install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). there is no package called data.table Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, 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. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 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. Why do academics stay as adjuncts for years rather than move around? 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. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: I was assuming that to be the case. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Is there anything I can do to speed it up? Running. 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 . in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so In addition: Warning message: installation of package GenomeInfoDbData had non-zero exit status. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Are there tables of wastage rates for different fruit and veg? 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 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'GenomeInfoDbData' Error: package 'GenomeInfoDb' could not be loaded Connect and share knowledge within a single location that is structured and easy to search. 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"). [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 R DESeq2 - [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. 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. Why is this sentence from The Great Gatsby grammatical? To add to this, I have also been using DESeq2 recently and ran into the same problem. Please remember to confirm an answer once you've received one. Loading required package: GenomicRanges Running under: Windows 10 x64 (build 18362), locale: I even tried BiocManager::install("XML") but all failed as shown below. library(DESeq2) 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. rev2023.3.3.43278. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Well occasionally send you account related emails. - the incident has nothing to do with me; can I use this this way? While a notebook is attached to a cluster, the R namespace cannot be refreshed. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Connect and share knowledge within a single location that is structured and easy to search. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Do I need a thermal expansion tank if I already have a pressure tank? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Author: Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd], Maintainer: Michael Love . March 1, 2023, 8:52pm Find centralized, trusted content and collaborate around the technologies you use most. Policy. I do know that it works well in qiime2-2020.6. Have a question about this project? [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 But I guess you have many problems with your installation, and I'd suggest. 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. Is there a proper earth ground point in this switch box? 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. Error when installing Aldex2 - Community Plugin Support - Open Source It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Sounds like there might be an issue with conda setup? @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. Running under: macOS Sierra 10.12.6. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Erasmus+ funds available! Solution To resolve this error, install the required package as a cluster-installed library. [a/s/n]: [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Resolving package or namespace loading error I also tried something I found on google: but the installation had errors too, I can write them here if needed. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Platform: x86_64-apple-darwin17.0 (64-bit) Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Rload failed - * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Bioconductor - DESeq2 Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. What do I need to do to reproduce your problem? March 1, 2023, 4:56pm 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 One solution is to find all available packages. I have tried your suggestion and also updating the packages that command indicates. I need help installing a package "DESeq2" having - RStudio Community DESeq2_2301_76497647-CSDN You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. May I know is there any other approach I can try? "htmlTable", "xfun" Try installing zip, and then loading olsrr. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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"). May be the version has problem How can I do ? 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 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Language(R, Python, SQL) If you try loading the DEseq2 library now, that might work. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Why do many companies reject expired SSL certificates as bugs in bug bounties? The error states that the current version is 0.4.5 but 0.4.10 is required. After 3-4 manual installs everything worked. Installing package(s) 'htmlTable', 'xfun' rev2023.3.3.43278. I'm trying to reproduce your problem, so being as precise as possible is important. I hope you can see something I can't see and help me solving this issue. 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: It only takes a minute to sign up. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Just updated my previous R to 4.01 and now I cant load DESeq2. 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 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!!! To learn more, see our tips on writing great answers. [16] phyloseq1.30.0, loaded via a namespace (and not attached): Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 1. I highly recommend that any R/RStudio version not installed inside conda be removed. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. If it fails, required operating system facilities are missing. Content type 'application/zip' length 4255589 bytes (4.1 MB) Follow Up: struct sockaddr storage initialization by network format-string. In install.packages() : Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): A place where magic is studied and practiced? Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? + "htmlTable", "xfun" 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") there is no package called locfit. 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. 9. R| - Give up and run everything from the "permitted" library location (e.g. Installation instructions to use this now when I tried installing the missing packages they did install. R version 3.6.3 (2020-02-29) Thanks for contributing an answer to Stack Overflow! Any other suggestion? I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open

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