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massimoaria / bibliometrix

An R-tool for comprehensive science mapping analysis. A package for quantitative research in scientometrics and bibliometrics.
https://www.bibliometrix.org
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bibliometrix on kaggle #345

Open dedtadeas opened 1 year ago

dedtadeas commented 1 year ago

Hi,

is there a way of running bibliometrix on kaggle? It gives me error due to R version.

Thank you! TD

massimoaria commented 1 year ago

Please provide us with more information about the issue.

dedtadeas commented 1 year ago

Hi,

sorry. Below is a Kaggle notebook code with outputs. The issue is that R version on Kaggle is 4.0.5, however, some packages require version >= 4.1.0. I will need to move from Kaggle to local to be able to run Bibliometrix. Thanks.

R.Version() $platform'x86_64-pc-linux-gnu'$arch'x86_64'$os'linux-gnu'$system'x86_64, linux-gnu'$status''$major'4'$minor'0.5'$year'2021'$month'03'$day'31'$svn rev'80133'$language'R'$version.string'R version 4.0.5 (2021-03-31)'$nickname'Shake and Throw' add Codeadd Markdown

devtools::install_github("massimoaria/bibliometrix", lib = "/kaggle/working") Downloading GitHub repo massimoaria/bibliometrix@HEAD

SnowballC (0.7.0 -> 0.7.1 ) [CRAN] vctrs (0.5.2 -> 0.6.2 ) [CRAN] rlang (1.0.6 -> 1.1.1 ) [CRAN] cli (3.6.0 -> 3.6.1 ) [CRAN] fs (1.6.1 -> 1.6.2 ) [CRAN] cachem (1.0.7 -> 1.0.8 ) [CRAN] htmltools (0.5.4 -> 0.5.5 ) [CRAN] hms (1.1.2 -> 1.1.3 ) [CRAN] pillar (1.8.1 -> 1.9.0 ) [CRAN] tibble (3.1.8 -> 3.2.1 ) [CRAN] openssl (2.0.5 -> 2.0.6 ) [CRAN] XML (3.99-0.13 -> 3.99-0.14) [CRAN] dplyr (1.1.0 -> 1.1.2 ) [CRAN] gtable (0.3.1 -> 0.3.3 ) [CRAN] ggplot2 (3.4.1 -> 3.4.2 ) [CRAN] tinytex (0.44 -> 0.45 ) [CRAN] fontawesome (0.5.0 -> 0.5.1 ) [CRAN] xfun (0.37 -> 0.39 ) [CRAN] rmarkdown (2.20 -> 2.21 ) [CRAN] htmlwidgets (1.6.1 -> 1.6.2 ) [CRAN] waldo (0.4.0 -> 0.5.0 ) [CRAN] ps (1.7.2 -> 1.7.5 ) [CRAN] processx (3.8.0 -> 3.8.1 ) [CRAN] testthat (3.1.6 -> 3.1.7 ) [CRAN] lme4 (1.1-31 -> 1.1-33 ) [CRAN] quantreg (5.94 -> 5.95 ) [CRAN] commonmark (1.8.1 -> 1.9.0 ) [CRAN] vroom (1.6.1 -> 1.6.3 ) [CRAN] rentrez (NA -> 1.2.3 ) [CRAN] zip (2.2.2 -> 2.3.0 ) [CRAN] scatterpl... (0.3-42 -> 0.3-43 ) [CRAN] multcompView (NA -> 0.1-9 ) [CRAN] flashClust (NA -> 1.01-2 ) [CRAN] ellipse (0.4.3 -> 0.4.5 ) [CRAN] car (NA -> 3.1-2 ) [CRAN] rscopus (NA -> 0.6.6 ) [CRAN] pubmedR (NA -> 0.0.3 ) [CRAN] igraph (1.4.1 -> 1.4.2 ) [CRAN] FactoMineR (NA -> 2.8 ) [CRAN] dimensionsR (NA -> 0.0.3 ) [CRAN] bibliomet... (NA -> 0.3.0 ) [CRAN] Skipping 2 packages not available: pbkrtest, emmeans

Installing 43 packages: SnowballC, vctrs, rlang, cli, fs, cachem, htmltools, hms, pillar, tibble, openssl, XML, dplyr, gtable, ggplot2, tinytex, fontawesome, xfun, rmarkdown, htmlwidgets, waldo, ps, processx, testthat, lme4, quantreg, pbkrtest, commonmark, vroom, rentrez, zip, scatterplot3d, multcompView, flashClust, emmeans, ellipse, car, rscopus, pubmedR, igraph, FactoMineR, dimensionsR, bibliometrixData

Warning message: “packages ‘pbkrtest’, ‘emmeans’ are not available for this version of R ‘emmeans’ version 1.8.5 is in the repositories but depends on R (>= 4.1.0) ‘pbkrtest’ version 0.5.2 is in the repositories but depends on R (>= 4.1.0)

Versions of these packages 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” Warning message: “dependencies ‘pbkrtest’, ‘emmeans’ are not available” Warning message in i.p(...): “installation of package ‘rlang’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘cli’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘fs’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘vctrs’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘gtable’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘car’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘pillar’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘tibble’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘dplyr’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘ggplot2’ had non-zero exit status” Warning message in i.p(...): “installation of package ‘FactoMineR’ had non-zero exit status” ── R CMD build ─────────────────────────────────────────────────────────────────

  1. devtools::install_github("massimoaria/bibliometrix", lib = "/kaggle/working")
  2. pkgbuild::with_build_tools({ . ellipsis::check_dots_used(action = getOption("devtools.ellipsis_action", . rlang::warn)) . { . remotes <- lapply(repo, github_remote, ref = ref, subdir = subdir, . auth_token = auth_token, host = host) . install_remotes(remotes, auth_token = auth_token, host = host, . dependencies = dependencies, upgrade = upgrade, force = force, . quiet = quiet, build = build, build_opts = build_opts, . build_manual = build_manual, build_vignettes = build_vignettes, . repos = repos, type = type, ...) . } . }, required = FALSE)
  3. install_remotes(remotes, auth_token = auth_token, host = host, . dependencies = dependencies, upgrade = upgrade, force = force, . quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual, . build_vignettes = build_vignettes, repos = repos, type = type, . ...)
  4. tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) { . stop(remote_install_error(remotes[[i]], e)) . })
  5. tryCatchList(expr, classes, parentenv, handlers)
  6. tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[3L]