Installation failure due to modes package

[avportal]

Hi there,

I am trying to install the package but I get the following error message:

ERROR: dependency ‘modes’ is not available for package ‘MicrobiomeR’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/MicrobiomeR’
Error: Failed to install 'MicrobiomeR' from GitHub:
  (converted from warning) installation of package ‘/var/folders/st/y2p98lbd0y58731wvyg2rgpc0000gp/T//RtmpI4UmRD/fileefb13850b96/MicrobiomeR_0.6.1.tar.gz’ had non-zero exit status

> install.packages("modes")
Warning in install.packages :
  package ‘modes’ is not available (for R version 3.6.3)

It seems that the package "modes" has been removed from the CRAN repository.

Insert Session info here

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] phyloseq_1.30.0 devtools_2.3.0  usethis_1.6.1  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6        ape_5.4             lattice_0.20-41    
 [4] prettyunits_1.1.1   ps_1.3.3            Biostrings_2.54.0  
 [7] assertthat_0.2.1    rprojroot_1.3-2     digest_0.6.25      
[10] foreach_1.5.0       R6_2.4.1            plyr_1.8.6         
[13] backports_1.1.7     stats4_3.6.3        ggplot2_3.3.1      
[16] pillar_1.4.4        zlibbioc_1.32.0     rlang_0.4.6        
[19] curl_4.3            rstudioapi_0.11     data.table_1.12.8  
[22] vegan_2.5-6         callr_3.4.3         S4Vectors_0.24.4   
[25] Matrix_1.2-18       splines_3.6.3       desc_1.2.0         
[28] stringr_1.4.0       igraph_1.2.5        munsell_0.5.0      
[31] compiler_3.6.3      pkgconfig_2.0.3     BiocGenerics_0.32.0
[34] multtest_2.42.0     pkgbuild_1.0.8      mgcv_1.8-31        
[37] tidyselect_1.1.0    biomformat_1.14.0   tibble_3.0.1       
[40] IRanges_2.20.2      codetools_0.2-16    permute_0.9-5      
[43] fansi_0.4.1         dplyr_1.0.0         crayon_1.3.4       
[46] withr_2.2.0         MASS_7.3-51.6       grid_3.6.3         
[49] nlme_3.1-148        jsonlite_1.6.1      gtable_0.3.0       
[52] lifecycle_0.2.0     magrittr_1.5        scales_1.1.1       
[55] cli_2.0.2           stringi_1.4.6       XVector_0.26.0     
[58] reshape2_1.4.4      fs_1.4.1            remotes_2.1.1      
[61] testthat_2.3.2      generics_0.0.2      ellipsis_0.3.1     
[64] vctrs_0.3.1         Rhdf5lib_1.8.0      iterators_1.0.12   
[67] tools_3.6.3         ade4_1.7-15         Biobase_2.46.0     
[70] glue_1.4.1          purrr_0.3.4         survival_3.1-12    
[73] processx_3.4.2      pkgload_1.1.0       parallel_3.6.3     
[76] colorspace_1.4-1    rhdf5_2.30.1        cluster_2.1.0      
[79] sessioninfo_1.1.1   memoise_1.1.0

[grabear]

Hi @avportal. I'm very sorry it took this long to get back to you fully. It seems that you are correct about the modes package. We only use one function from there (shown below). It shouldn't be to hard to port it over, and remove the modes as a dependency completely. I will work on this tomorrow and try to get the changes update for you.

bimodality_coefficient<-function(x, finite=TRUE,...){
	if(finite==TRUE){
		G=skewness(x,finite)
		sample.excess.kurtosis=kurtosis(x,finite)
		K=sample.excess.kurtosis
		n=length(x)
		B=((G^2)+1)/(K+ ((3*((n-1)^2))/((n-2)*(n-3))))
	}
	else{
		G=skewness(x,FALSE)
		K=kurtosis(x,FALSE)
		B=((G^2)+1)/(K)
	}
	return(B)
}

[grabear]

https://github.com/sathish-deevi/modes-Package/blob/master/src/R/Nonparametric_functions.R

[sdhutchins]

@grabear I created this little branch for that. Feel free to delete it. 😃

[avportal]

Thank you! Cheers, Angel

…

On 08 Jul 2020, at 01:12, Rob Gilmore ***@***.***> wrote: Hi @avportal <https://github.com/avportal>. I'm very sorry it took this long to get back to you fully. It seems that you are correct about the modes package. We only use one function from there (shown below). It shouldn't be to hard to port it over, and remove the modes as a dependency completely. I will work on this tomorrow and try to get the changes update for you. bimodality_coefficient<-function(x, finite=TRUE,...){ if(finite==TRUE){ G=skewness(x,finite) sample.excess.kurtosis=kurtosis(x,finite) K=sample.excess.kurtosis n=length(x) B=((G^2)+1)/(K+ ((3*((n-1)^2))/((n-2)*(n-3)))) } else{ G=skewness(x,FALSE) K=kurtosis(x,FALSE) B=((G^2)+1)/(K) } return(B) } — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#105 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AO4MKESZJR3YC3PALALNWILR2OTWZANCNFSM4N5LG6UQ>.

___________________ Angel Valverde Portal IRNASA-CSIC C/ Cordel de Merinas 40-52 37008 Salamanca Spain Tel.: +34 923 219 606

[sdhutchins]

@avportal I would suggest installing this release with the latest version of R (4.0).

MicrobiomeR_0.7.0.tar.gz

install.packages("MicrobiomeR_0.7.0.tar.gz", repos = NULL, type ="source")

[avportal]

Many thanks. Regards, Angel

…

On 09 Aug 2020, at 05:21, Shaurita Hutchins ***@***.***> wrote: @avportal <https://github.com/avportal> I would suggest installing this release <https://github.com/vallenderlab/MicrobiomeR/releases/tag/v0.7.0> with the latest version of R (4.0). MicrobiomeR_0.7.0.tar.gz <https://github.com/vallenderlab/MicrobiomeR/files/5046711/MicrobiomeR_0.7.0.tar.gz> install.packages("MicrobiomeR_0.7.0.tar.gz", repos = NULL, type =‘‘source’’) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#105 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AO4MKETVGLKCPZ3O7HXNHVDR7YI3XANCNFSM4N5LG6UQ>.

___________________ Angel Valverde Portal IRNASA-CSIC C/ Cordel de Merinas 40-52 37008 Salamanca Spain Tel.: +34 923 219 606 (Ext. 231) Fax: +34 923 219 609 angel.valverde@csic.es

[lixiaopi1985]

work around: download modes package from CRAN: https://cran.r-project.org/web/packages/modes/index.html, and install it locally install_local()

[grabear]

@lixiaopi1985 Thank you for this workaround. @sdhutchins And thank you for pushing a working release.

@avportal The issue should be fixed by installing MicrobiomeR using @sdhutchins solution. If you have any more issues with this, then please let us know.

The primary reason for the delay with this bug fix was a failure to get our Travis CI and GitHub actions working properly. However, this is a separate issue and should have been treated as one.