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

[Martin Morgan]

Likely you or one of your dependent packages makes use of Matrix without 
using import() in the NAMESPACE file.

Email formatting makes it hard to tell exactly what is going on; make 
sure you are sending email in plain text, and that the build / check 
steps are done at the command line rather than through tools within R.

Martin

On 08/20/2017 04:16 PM, Arman Shahrisa wrote:
> 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.
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> Sincerely,
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> Arman
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> ==> roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace', 'vignette'))
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> Updating vignettes
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> Documentation completed
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> ==> Rcmd.exe build cbaf
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> * checking for file 'cbaf/DESCRIPTION' ... OK
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> * preparing 'cbaf':
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> * checking DESCRIPTION meta-information ... OK
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> * installing the package to build vignettes
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> * creating vignettes ... OK
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> * checking for LF line-endings in source and make files
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> * checking for empty or unneeded directories
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> * building 'cbaf_0.99.1.tar.gz'
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> 
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> ==> Rcmd.exe check cbaf_0.99.1.tar.gz
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> 
> * using log directory 'Z:/cbaf/Source code/cbaf.Rcheck'
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> * using R version 3.4.1 (2017-06-30)
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> * using platform: x86_64-w64-mingw32 (64-bit)
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> * using session charset: ISO8859-1
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> * checking for file 'cbaf/DESCRIPTION' ... OK
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> * this is package 'cbaf' version '0.99.1'
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> * package encoding: UTF-8
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> * checking package namespace information ... OK
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> * checking package dependencies ... OK
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> * checking if this is a source package ... OK
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> * checking if there is a namespace ... OK
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> * checking for executable files ... OK
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> * checking for hidden files and directories ... OK
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> * checking for portable file names ... OK
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> * checking whether package 'cbaf' can be installed ... OK
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> * checking installed package size ... OK
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> * checking package directory ... OK
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> * checking 'build' directory ... OK
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> * checking DESCRIPTION meta-information ... OK
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> * checking top-level files ... OK
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> * checking for left-over files ... OK
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> * checking index information ... OK
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> * checking package subdirectories ... OK
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> * checking R files for non-ASCII characters ... OK
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> * checking R files for syntax errors ... OK
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> * checking whether the package can be loaded ... OK
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> * checking whether the package can be loaded with stated dependencies ... OK
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> * checking whether the package can be unloaded cleanly ... OK
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> * checking whether the namespace can be loaded with stated dependencies ... OK
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> * checking whether the namespace can be unloaded cleanly ... OK
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> * checking loading without being on the library search path ... WARNING
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> Error: package or namespace load failed for 'cbaf' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
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>   there is no package called 'Matrix'
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> Execution halted
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> It looks like this package has a loading problem when not on .libPaths:
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> see the messages for details.
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> * checking dependencies in R code ... OK
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> * checking S3 generic/method consistency ... OK
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> * checking replacement functions ... OK
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> * checking foreign function calls ... OK
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> * checking R code for possible problems ... OK
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> * checking Rd files ... OK
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> * checking Rd metadata ... OK
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> * checking Rd cross-references ... OK
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> * checking for missing documentation entries ... OK
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> * checking for code/documentation mismatches ... OK
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> * checking Rd \usage sections ... OK
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> * checking Rd contents ... OK
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> * checking for unstated dependencies in examples ... OK
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> * checking installed files from 'inst/doc' ... OK
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> * checking files in 'vignettes' ... OK
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> * checking examples ... OK
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> * checking for unstated dependencies in vignettes ... OK
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> * checking package vignettes in 'inst/doc' ... OK
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> * checking running R code from vignettes ...
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>     'cbaf.Rmd' using 'UTF-8' ... OK
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>   NONE
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> * checking re-building of vignette outputs ... OK
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> * checking PDF version of manual ... OK
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> * DONE
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> Status: 1 WARNING
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> See
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>    'Z:/cbaf/Source code/cbaf.Rcheck/00check.log'
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> for details.
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> R CMD check succeeded
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> 	[[alternative HTML version deleted]]
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