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This page was generated on 2023-10-20 09:38:01 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 559/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diggit 1.32.0  (landing page)
Mariano J Alvarez
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/diggit
git_branch: RELEASE_3_17
git_last_commit: 1261d37
git_last_commit_date: 2023-04-25 10:38:05 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for diggit on kjohnson2


To the developers/maintainers of the diggit package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: diggit
Version: 1.32.0
Command: /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
StartedAt: 2023-10-17 15:55:23 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 16:00:19 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 295.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: diggit.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /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.



Installation output

diggit.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL diggit
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)

Tests output


Example timings

diggit.Rcheck/diggit-Ex.timings

nameusersystemelapsed
aqtl-methods15.810 0.98225.029
conditional-methods16.093 0.94723.934
correlation0.0010.0010.001
diggit-class1.6910.0522.659
diggit-methods5.5950.2348.876
diggit-plot16.096 0.96925.950
fcnv-methods1.7910.0682.842
marina-methods87.25113.33273.550
mutualInfo2.5120.0953.796