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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diggit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diggit_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/diggit.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diggit/DESCRIPTION’ ... OK
* this is package ‘diggit’ version ‘1.32.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘diggit’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in citeEntry(entry = "article", author = c(person(c("Mariano", "J"), "Alvarez"), person(c("James", "C"), "Chen"), person("Andrea", "Califano")), title = "{DIGGIT}: a Bioconductor package to infer genetic variants driving cellular phenotypes", journal = "Bioinformatics", year = 2015, volume = 31, number = 24, pages = "4032--4", textVersion = "Alvarez, M.J., Chen, J.C., and Califano, A. (2015) DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics 31(24):4032--4."): could not find function "citeEntry"
* 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 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
aecdf: no visible global function definition for ‘quantile’
aecdf: no visible global function definition for ‘ecdf’
aecdf: no visible global function definition for ‘knots’
aecdf: no visible global function definition for ‘lm’
aecdf: no visible global function definition for ‘approxfun’
aecdf : dnull: no visible global function definition for ‘predict’
aecdf : dnull: no visible global function definition for ‘qnorm’
conditionalInternal: no visible global function definition for
‘p.adjust’
conditionalInternal : <anonymous>: no visible global function
definition for ‘fisher.test’
conditionalInternal: no visible global function definition for ‘hclust’
conditionalInternal: no visible global function definition for
‘as.dist’
conditionalInternal: no visible global function definition for ‘cutree’
conditionalInternal : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for ‘fisher.test’
conditionalInternal : <anonymous> : <anonymous>: no visible global
function definition for ‘fisher.test’
correlation : <anonymous>: no visible global function definition for
‘cor’
correlation: no visible global function definition for ‘cor’
cortest: no visible global function definition for ‘pnorm’
distMode: no visible global function definition for ‘density’
fet: no visible global function definition for ‘fisher.test’
internalMIfb: no visible global function definition for ‘dnorm’
mutualInfo: no visible global function definition for ‘qnorm’
mutualInfo: no visible global function definition for ‘combn’
mutualInfo: no visible global function definition for ‘txtProgressBar’
mutualInfo : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
plothm: no visible global function definition for ‘rgb2hsv’
plothm: no visible global function definition for ‘col2rgb’
plothm: no visible global function definition for ‘hsv’
plothm: no visible global function definition for ‘image’
plothm: no visible global function definition for ‘box’
aqtl,diggit: no visible global function definition for ‘p.adjust’
aqtl,diggit: no visible global function definition for ‘pnorm’
conditional,diggit: no visible global function definition for
‘p.adjust’
conditional,diggit: no visible global function definition for ‘pnorm’
conditional,diggit: no visible global function definition for
‘txtProgressBar’
conditional,diggit : <anonymous>: no visible global function definition
for ‘setTxtProgressBar’
marina,matrix: no visible global function definition for ‘qnorm’
mindyFiltering,diggit: no visible global function definition for
‘p.adjust’
plot,diggit-ANY: no visible global function definition for ‘abline’
plot,diggit-ANY: no visible global function definition for ‘text’
plot,diggit-ANY: no visible global function definition for ‘axis’
Undefined global functions or variables:
abline approxfun as.dist axis box col2rgb combn cor cutree density
dnorm ecdf fisher.test hclust hsv image knots lm p.adjust pnorm
predict qnorm quantile rgb2hsv setTxtProgressBar text txtProgressBar
Consider adding
importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
importFrom("graphics", "abline", "axis", "box", "image", "text")
importFrom("stats", "approxfun", "as.dist", "cor", "cutree", "density",
"dnorm", "ecdf", "fisher.test", "hclust", "knots", "lm",
"p.adjust", "pnorm", "predict", "qnorm", "quantile")
importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'plot' and siglist 'diggit,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'aecdf':
aecdf
Code: function(dnull, symmetric = FALSE, n = 100)
Docs: function(dnull, symmetric = FALSE)
Argument names in code not in docs:
n
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
marina-methods 87.251 13.332 73.550
diggit-plot 16.096 0.969 25.950
conditional-methods 16.093 0.947 23.934
aqtl-methods 15.810 0.982 25.029
diggit-methods 5.595 0.234 8.876
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/diggit.Rcheck/00check.log’
for details.
