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CHECK report for diggit on tokay1

This page was generated on 2019-04-13 11:25:00 -0400 (Sat, 13 Apr 2019).

Package 414/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diggit 1.14.0
Mariano J Alvarez
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/diggit
Branch: RELEASE_3_8
Last Commit: 038aa4d
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: diggit
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diggit.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings diggit_1.14.0.tar.gz
StartedAt: 2019-04-13 01:49:56 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:57:28 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 452.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: diggit.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diggit.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings diggit_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/diggit.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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: no visible global function definition for 'abline'
plot,diggit: no visible global function definition for 'text'
plot,diggit: 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 ... OK
* 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      85.85  14.03   99.89
aqtl-methods        12.90   1.52   14.42
diggit-plot         14.01   0.34   14.36
conditional-methods 12.78   0.56   13.34
diggit-methods       6.47   0.11    6.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
marina-methods      98.47  13.23  111.70
conditional-methods 14.67   0.36   15.03
aqtl-methods        13.95   0.88   14.83
diggit-plot         13.76   0.32   14.08
diggit-methods       5.83   0.35    6.19
* 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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/diggit.Rcheck/00check.log'
for details.



Installation output

diggit.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/diggit_1.14.0.tar.gz && rm -rf diggit.buildbin-libdir && mkdir diggit.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diggit.buildbin-libdir diggit_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL diggit_1.14.0.zip && rm diggit_1.14.0.tar.gz diggit_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 26402  100 26402    0     0   314k      0 --:--:-- --:--:-- --:--:--  330k

install for i386

* installing *source* package 'diggit' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'diggit' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diggit' as diggit_1.14.0.zip
* DONE (diggit)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'diggit' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

diggit.Rcheck/examples_i386/diggit-Ex.timings

nameusersystemelapsed
aqtl-methods12.90 1.5214.42
conditional-methods12.78 0.5613.34
correlation000
diggit-class2.030.002.03
diggit-methods6.470.116.58
diggit-plot14.01 0.3414.36
fcnv-methods2.050.052.09
marina-methods85.8514.0399.89
mutualInfo2.060.002.06

diggit.Rcheck/examples_x64/diggit-Ex.timings

nameusersystemelapsed
aqtl-methods13.95 0.8814.83
conditional-methods14.67 0.3615.03
correlation000
diggit-class1.610.081.68
diggit-methods5.830.356.19
diggit-plot13.76 0.3214.08
fcnv-methods1.770.031.80
marina-methods 98.47 13.23111.70
mutualInfo3.140.003.14