fontikar / mvabund Goto Github PK

Upon running check()

  There is circular dependency in the installation order:
    One or more packages in
    'Rcpp', 'MASS', 'methods', 'stats', 'tweedie', 'statmod', 'parallel',
    'ecostats', 'RcppGSL', 'utils', 'grDevices', 'graphics', 'ecoCopula',
    'GET', 'mgcv', 'mvtnorm', 'glasso', 'plyr', 'sna', 'igraph',
    'betareg', 'doParallel', 'glm2', 'ordinal', 'compiler', 'foreach',
    'cluster', 'ggplot2', 'gridExtra', 'viridisLite', 'nlme', 'Matrix',
    'splines', 'statnet.common', 'network', 'magrittr', 'pkgconfig',
    'rlang', 'flexmix', 'Formula', 'lmtest', 'modeltools', 'sandwich',
    'iterators', 'ucminf', 'numDeriv', 'codetools', 'digest', 'glue',
    'grid', 'gtable', 'isoband', 'scales', 'tibble', 'withr', 'lattice',
    'coda', 'tools', 'nnet', 'stats4', 'zoo', 'farver', 'labeling',
    'lifecycle', 'munsell', 'R6', 'RColorBrewer', 'ellipsis', 'fansi',
    'pillar', 'vctrs', 'colorspace', 'cli', 'utf8'
    depend on this package (for the versions on the repositories).

@dwarton any idea which package in this list depends/suggests/imports mvabund

Locally on my computer, the pkgdown site renders beautifully

Website is not rendering as Github pages - https://fontikar.github.io/mvabund/

I thought it may have to do with whether the site the in development or released mode: https://pkgdown.r-lib.org/articles/how-to-update-released-site.html

But doesn't seem to be as my other pkgdown projects are all set to "auto"

@dfalster do you have any ideas about this? Google with no success as I don't know what to refer to the 'unrendered, bare bones' state. Thank you in advance!!!

Tests and checks

-[] Currently not passing devtools::check

Documentation

• Update NAMESPACE for it to be controlled by roxygen2
• LazyData
• Improve README *
• Create vignette *
• Set up pkgdown

Continuous integration

• Replace travis and set up Github Actions for continuous testing
• More Github action workflows R CMD Check on different platforms
• Set up test coverage

Fluff upgrades

• Create a hex sticker

• = main priority

Re-compiling mvabund
─ installing source package ‘mvabund’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppGSL/include' -I/usr/local/include -fPIC -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppGSL/include/RcppGSL.h:25:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppGSL/include/RcppGSLForward.h:25:10: fatal error: 'gsl/gsl_vector.h' file not found
#include <gsl/gsl_vector.h>
^~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘mvabund’
─ removing ‘/private/var/folders/fk/9s3srn850qj90zp4t67zc0fm0000gq/T/RtmpRycsUY/devtools_install_f34412103db/mvabund’
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command 'R' failed, exit status: 1, stdout & stderr were printed
Type .Last.error.trace to see where the error occurred
In addition: Warning message:
No 'gsl-config' config script found, limiting extensibility.

Not sure where I can get these files got gsl/gsl-config.
I tried to install via homebrew and update Rccpgsl - no luck!

I will not worry for now! Can still make vignettes for now!