Error in polyglot evaluation. Can't accept parameters

[jobdiogenes]

Hi,

I could install with no problems package 'bibliometrix' in graalvm (20.1) and (20.3-dev) In both, I could load

library("bibliometrix")

but, when try to call

 biblioshiny(host="172.17.0.2",port=9999,launch.browser=FALSE)
Error in polyglot evaluation : Error in biblioshiny(host = "172.17.0.2", port = 9999, launch.browser = FALSE) :
  unused argument (host = "172.17.0.2")

fail and in exiting R, give a core dump.

[Alain-Bearez]

Most probably part of your above statement might be incorrect as installation of bibliometrix depends on several other packages among which shiny for which I reported an unsuccessful installation.

When trying to install the bibliometrix package on my GraalVM with FastR docker image, here was the reported list:

docker run --rm -ti cuali/fastr Rscript -e "install.packages('bibliometrix')"

also installing the dependencies 'sys', 'utf8', 'backports', 'zeallot', 'SparseM', 'MatrixModels', 'sp', 'minqa', 'nloptr', 'farver', 'colorspace', 'clipr', 'rematch', 'prettyunits',
 'askpass', 'cli', 'fansi', 'pillar', 'purrr', 'yaml', 'ggsci', 'cowplot', 'ggsignif', 'gridExtra', 'polynom', 'ellipsis', 'vctrs', 'lifecycle', 'carData', 'pbkrtest', 'quantreg',
 'maptools', 'lme4', 'tweenr', 'polyclip', 'RcppEigen', 'labeling', 'munsell', 'RcppArmadillo', 'forcats', 'hms', 'readr', 'cellranger', 'progress', 'zip', 'openssl', 'assertthat',
 'glue', 'pkgconfig', 'tibble', 'tidyselect', 'plogr', 'htmlwidgets', 'crosstalk', 'abind', 'dendextend', 'ggpubr', 'tidyr', 'car', 'ellipse', 'flashClust', 'leaps', 'scatterplot3d',
 'ggforce', 'scales', 'gtable', 'viridis', 'tidygraph', 'graphlayouts', 'lazyeval', 'mgcv', 'viridisLite', 'withr', 'plyr', 'haven', 'curl', 'readxl', 'openxlsx', 'httr', 'stringi',
 'dplyr', 'DT', 'factoextra', 'FactoMineR', 'ggraph', 'ggplot2', 'ggrepel', 'igraph', 'networkD3', 'reshape2', 'RColorBrewer', 'rio', 'RISmed', 'rscopus',
 'shiny', 'shinycssloaders', 'shinythemes', 'SnowballC', 'stringdist', 'stringr'

This is why I would like you to double check on your affirmation "I could install with no problems package 'bibliometrix' in graalvm" to check if no ERROR: was reported for any of the packages bibliometrix depends on.

[jobdiogenes]

Most probably part of your above statement might be incorrect as installation of bibliometrix depends on several other packages among which shiny for which I reported an unsuccessful installation.

When trying to install the bibliometrix package on my GraalVM with FastR docker image, here was the reported list:

docker run --rm -ti cuali/fastr Rscript -e "install.packages('bibliometrix')"

also installing the dependencies 'sys', 'utf8', 'backports', 'zeallot', 'SparseM', 'MatrixModels', 'sp', 'minqa', 'nloptr', 'farver', 'colorspace', 'clipr', 'rematch', 'prettyunits',
 'askpass', 'cli', 'fansi', 'pillar', 'purrr', 'yaml', 'ggsci', 'cowplot', 'ggsignif', 'gridExtra', 'polynom', 'ellipsis', 'vctrs', 'lifecycle', 'carData', 'pbkrtest', 'quantreg',
 'maptools', 'lme4', 'tweenr', 'polyclip', 'RcppEigen', 'labeling', 'munsell', 'RcppArmadillo', 'forcats', 'hms', 'readr', 'cellranger', 'progress', 'zip', 'openssl', 'assertthat',
 'glue', 'pkgconfig', 'tibble', 'tidyselect', 'plogr', 'htmlwidgets', 'crosstalk', 'abind', 'dendextend', 'ggpubr', 'tidyr', 'car', 'ellipse', 'flashClust', 'leaps', 'scatterplot3d',
 'ggforce', 'scales', 'gtable', 'viridis', 'tidygraph', 'graphlayouts', 'lazyeval', 'mgcv', 'viridisLite', 'withr', 'plyr', 'haven', 'curl', 'readxl', 'openxlsx', 'httr', 'stringi',
 'dplyr', 'DT', 'factoextra', 'FactoMineR', 'ggraph', 'ggplot2', 'ggrepel', 'igraph', 'networkD3', 'reshape2', 'RColorBrewer', 'rio', 'RISmed', 'rscopus',
 'shiny', 'shinycssloaders', 'shinythemes', 'SnowballC', 'stringdist', 'stringr'

This is why I would like you to double check on your affirmation "I could install with no problems package 'bibliometrix' in graalvm" to check if no ERROR: was reported for any of the packages bibliometrix depends on.

Well, I could install bibliometrix and load with library. Only when try to call biblioshiny with parameters I got that bizarre errors. Could be a fail in shiny execution, but was not a fail install.

shiny was also installed with no error.

` installing source* package ?shiny? ... package ?shiny? successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading help * installing help indices building package indices testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path

• DONE (shiny)

The downloaded source packages are in ?/tmp/RtmpuOJtnS/downloaded_packages? Updating HTML index of packages in '.Library' Making 'packages.html' ... done`

[Alain-Bearez]

May I ask which operating system you are using? I could try to build my FastR docker image based on that one instead of Oracle Linux 8 where shiny and dplyr consistently fail to install.

[jobdiogenes]

You could use one these docker images that I build and maintain, latest ce stable docker pull jobdiogenes/fastr or latest ce dev docker pull jobdiogenes/fastr:dev both build with debian-stable

I will also upload these two Dockerfiles to github.