Package: diggit

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diggit.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings diggit_1.18.0.tar.gz

StartedAt: 2020-04-15 02:42:16 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:49:11 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 414.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: diggit.Rcheck

Warnings: 3

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diggit.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings diggit_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/diggit.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'diggit/DESCRIPTION' ... OK
* this is package 'diggit' version '1.18.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
marina-methods      93.29  10.60  103.87
aqtl-methods        19.14   2.46   25.17
conditional-methods 16.13   2.15   18.28
diggit-plot         13.44   0.50   13.94
diggit-methods       6.65   0.22    6.90
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
marina-methods      79.96  18.76   98.92
conditional-methods 14.20   1.01   15.30
aqtl-methods        13.38   0.52   13.92
diggit-plot         12.66   0.78   13.44
diggit-methods       5.33   0.23    5.57
* 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
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/diggit.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/diggit_1.18.0.tar.gz && rm -rf diggit.buildbin-libdir && mkdir diggit.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diggit.buildbin-libdir diggit_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL diggit_1.18.0.zip && rm diggit_1.18.0.tar.gz diggit_1.18.0.zip
###
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install for i386

* installing *source* package 'diggit' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'diggit'
    finding HTML links ... done
    aecdf                                   html  
    aqtl-methods                            html  
    conditional-methods                     html  
    correlation                             html  
    diggit-class                            html  
    diggit-methods                          html  
    diggit-plot                             html  
    fcnv-methods                            html  
    marina-methods                          html  
    mutualInfo                              html  
** 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

install for x64

* installing *source* package 'diggit' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diggit' as diggit_1.18.0.zip
* DONE (diggit)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'diggit' successfully unpacked and MD5 sums checked