[Bioc-devel] Warning for Matrix during R CMD Check

[Arman Shahrisa]

Recently, I’m getting this warning. What is the cause? I have the package “Matrix” installed. Sometimes I get an error for the package “Matrix” during build. But today, it’s all about R CMD check.





Sincerely,

Arman













==> roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace', 'vignette'))



Updating vignettes

Documentation completed



==> Rcmd.exe build cbaf



* checking for file 'cbaf/DESCRIPTION' ... OK

* preparing 'cbaf':

* checking DESCRIPTION meta-information ... OK

* installing the package to build vignettes

* creating vignettes ... OK

* checking for LF line-endings in source and make files

* checking for empty or unneeded directories

* building 'cbaf_0.99.1.tar.gz'



==> Rcmd.exe check cbaf_0.99.1.tar.gz



* using log directory 'Z:/cbaf/Source code/cbaf.Rcheck'

* using R version 3.4.1 (2017-06-30)

* using platform: x86_64-w64-mingw32 (64-bit)

* using session charset: ISO8859-1

* checking for file 'cbaf/DESCRIPTION' ... OK

* this is package 'cbaf' version '0.99.1'

* package encoding: UTF-8

* checking package namespace information ... OK

* checking package dependencies ... OK

* checking if this is a source package ... OK

* checking if there is a namespace ... OK

* checking for executable files ... OK

* checking for hidden files and directories ... OK

* checking for portable file names ... OK

* checking whether package 'cbaf' can be installed ... OK

* checking installed package size ... OK

* checking package directory ... OK

* checking 'build' directory ... OK

* checking DESCRIPTION meta-information ... OK

* checking top-level files ... OK

* checking for left-over files ... OK

* checking index information ... OK

* checking package subdirectories ... OK

* checking R files for non-ASCII characters ... OK

* checking R files for syntax errors ... OK

* checking whether the package can be loaded ... OK

* checking whether the package can be loaded with stated dependencies ... OK

* checking whether the package can be unloaded cleanly ... OK

* checking whether the namespace can be loaded with stated dependencies ... OK

* checking whether the namespace can be unloaded cleanly ... OK

* checking loading without being on the library search path ... WARNING

Error: package or namespace load failed for 'cbaf' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called 'Matrix'

Execution halted



It looks like this package has a loading problem when not on .libPaths:

see the messages for details.

* checking dependencies in R code ... OK

* checking S3 generic/method consistency ... OK

* checking replacement functions ... OK

* checking foreign function calls ... OK

* checking R code for possible problems ... OK

* checking Rd files ... OK

* checking Rd metadata ... OK

* checking Rd cross-references ... OK

* checking for missing documentation entries ... OK

* checking for code/documentation mismatches ... OK

* checking Rd \usage sections ... OK

* checking Rd contents ... OK

* checking for unstated dependencies in examples ... OK

* checking installed files from 'inst/doc' ... OK

* checking files in 'vignettes' ... OK

* checking examples ... OK

* checking for unstated dependencies in vignettes ... OK

* checking package vignettes in 'inst/doc' ... OK

* checking running R code from vignettes ...

   'cbaf.Rmd' using 'UTF-8' ... OK

 NONE

* checking re-building of vignette outputs ... OK

* checking PDF version of manual ... OK

* DONE

Status: 1 WARNING



See

  'Z:/cbaf/Source code/cbaf.Rcheck/00check.log'

for details.





R CMD check succeeded



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