Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:06:30 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for diggit on tokay2


To the developers/maintainers of the diggit package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diggit.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 512/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diggit 1.26.0  (landing page)
Mariano J Alvarez
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/diggit
git_branch: RELEASE_3_14
git_last_commit: 73cd356
git_last_commit_date: 2021-10-26 12:19:08 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: diggit
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diggit.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings diggit_1.26.0.tar.gz
StartedAt: 2022-01-18 18:34:40 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 18:41:22 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 402.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: diggit.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diggit.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings diggit_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/diggit.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.26.0'
* 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 (user + system) or elapsed time > 5s
                     user system elapsed
marina-methods      83.57  14.67   98.25
aqtl-methods        14.06   1.57   16.44
conditional-methods 13.90   1.46   15.36
diggit-plot         13.52   1.07   14.60
diggit-methods       6.39   0.21    6.65
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
marina-methods      82.00  15.85   97.84
diggit-plot         13.36   0.83   14.19
aqtl-methods        11.98   1.38   13.36
conditional-methods 12.09   0.31   12.40
diggit-methods       5.34   0.15    5.50
* 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-3.14-bioc/meat/diggit.Rcheck/00check.log'
for details.



Installation output

diggit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/diggit_1.26.0.tar.gz && rm -rf diggit.buildbin-libdir && mkdir diggit.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diggit.buildbin-libdir diggit_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL diggit_1.26.0.zip && rm diggit_1.26.0.tar.gz diggit_1.26.0.zip
###
##############################################################################
##############################################################################


  % 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 25961  100 25961    0     0   307k      0 --:--:-- --:--:-- --:--:--  312k

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_1.26.0.zip
* DONE (diggit)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'diggit' successfully unpacked and MD5 sums checked

Tests output


Example timings

diggit.Rcheck/examples_i386/diggit-Ex.timings

nameusersystemelapsed
aqtl-methods14.06 1.5716.44
conditional-methods13.90 1.4615.36
correlation000
diggit-class2.090.012.11
diggit-methods6.390.216.65
diggit-plot13.52 1.0714.60
fcnv-methods2.450.052.50
marina-methods83.5714.6798.25
mutualInfo1.850.021.87

diggit.Rcheck/examples_x64/diggit-Ex.timings

nameusersystemelapsed
aqtl-methods11.98 1.3813.36
conditional-methods12.09 0.3112.40
correlation000
diggit-class1.520.101.61
diggit-methods5.340.155.50
diggit-plot13.36 0.8314.19
fcnv-methods1.690.091.78
marina-methods82.0015.8597.84
mutualInfo2.180.012.21