rstudio@cafc4643c5a5:~$ R CMD check NanoStringNCTools_1.11.4.tar.gz --no-manual
* using log directory ‘/home/rstudio/NanoStringNCTools.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘NanoStringNCTools/DESCRIPTION’ ... OK
* this is package ‘NanoStringNCTools’ version ‘1.11.4’
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘NanoStringNCTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* 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 ... NOTE
autoplot.NanoStringRccSet : <anonymous>: warning in switch(x[2], A =
qcCutoffs[["BindingDensity"]][["maximumBD"]], B =
qcCutoffs[["BindingDensity"]][["maximumBD"]], C =
qcCutoffs[["BindingDensity"]][["maximumBD"]], D =
qcCutoffs[["BindingDensity"]][["maximumBD"]], E =
qcCutoffs[["BindingDensity"]][["maximumBD"]], G =
qcCutoffs[["BindingDensity"]][["maximumBD"]], H =
qcCutoffs[["BindingDensity"]][["maximumBD"]], P =
qcCutoffs[["BindingDensity"]][["maximumBDSprint"]], default =
qcCutoffs[["BindingDensity"]][["maximumBD"]]): partial argument match
of 'E' to 'EXPR'
setQCFlags,NanoStringRccSet : <anonymous>: warning in switch(x[2], A =
maxBindDen, B = maxBindDen, C = maxBindDen, D = maxBindDen, E =
maxBindDen, G = maxBindDen, H = maxBindDen, P = maxBindDenSprint,
default = maxBindDen): partial argument match of 'E' to 'EXPR'
autoplot.NanoStringRccSet: no visible binding for global variable
‘xend’
autoplot.NanoStringRccSet: no visible binding for global variable
‘passingThreshold’
autoplot.NanoStringRccSet: no visible binding for global variable
‘GeomMean’
autoplot.NanoStringRccSet: no visible binding for global variable ‘h’
autoplot.NanoStringRccSet: no visible binding for global variable
‘label’
Undefined global functions or variables:
GeomMean h label passingThreshold xend
* 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 ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘Introduction.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* DONE
Status: 4 NOTEs
See
‘/home/rstudio/NanoStringNCTools.Rcheck/00check.log’
for details.
Update man pages for updated roxygen warnings