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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:diggit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings diggit_1.39.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/diggit.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘diggit/DESCRIPTION’ ... OK
* this is package ‘diggit’ version ‘1.39.0’
* 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 code 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
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 Rd file 'aecdf.Rd':
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
marina-methods      94.579 16.130  38.138
conditional-methods 11.894  0.305  12.199
aqtl-methods        11.460  0.487  11.955
diggit-plot         11.700  0.182  11.882
diggit-methods       5.133  0.242   5.377
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/diggit.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL diggit
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘diggit’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (diggit)