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BioC 3.4: CHECK report for diggit on moscato1

This page was generated on 2016-09-21 03:46:52 -0700 (Wed, 21 Sep 2016).

Package 321/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diggit 1.5.2
Mariano J Alvarez
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/diggit
Last Changed Rev: 120591 / Revision: 121152
Last Changed Date: 2016-08-30 13:33:12 -0700 (Tue, 30 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: diggit
Version: 1.5.2
Command: rm -rf diggit.buildbin-libdir diggit.Rcheck && mkdir diggit.buildbin-libdir diggit.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=diggit.buildbin-libdir diggit_1.5.2.tar.gz >diggit.Rcheck\00install.out 2>&1 && cp diggit.Rcheck\00install.out diggit-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=diggit.buildbin-libdir --install="check:diggit-install.out" --force-multiarch --no-vignettes --timings diggit_1.5.2.tar.gz
StartedAt: 2016-09-20 07:10:58 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:17:52 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 414.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: diggit.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf diggit.buildbin-libdir diggit.Rcheck && mkdir diggit.buildbin-libdir diggit.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=diggit.buildbin-libdir diggit_1.5.2.tar.gz >diggit.Rcheck\00install.out 2>&1 && cp diggit.Rcheck\00install.out diggit-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=diggit.buildbin-libdir --install="check:diggit-install.out" --force-multiarch --no-vignettes --timings diggit_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/diggit.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.5.2'
* 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 eval(expr, envir, enclos): 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
** checking loading without being on the library search path ... 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 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 : 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 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", "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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... 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      103.52   6.52  110.06
diggit-plot          17.66   0.16   17.81
conditional-methods  17.00   0.53   17.54
aqtl-methods         16.22   0.36   21.34
diggit-methods        6.37   0.06    6.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
marina-methods      100.17   7.22  107.41
conditional-methods  18.47   0.19   18.65
diggit-plot          16.77   0.09   16.86
aqtl-methods         15.28   0.25   15.53
diggit-methods        6.26   0.08    6.33
* 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: 1 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/diggit.Rcheck/00check.log'
for details.


diggit.Rcheck/00install.out:


install for i386

* installing *source* package 'diggit' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'diggit'
Creating a generic function for 'summary' from package 'base' in package 'diggit'
Creating a generic function for 'head' from package 'utils' in package 'diggit'
Creating a generic function for 'plot' from package 'graphics' in package 'diggit'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'diggit' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diggit' as diggit_1.5.2.zip
* DONE (diggit)

diggit.Rcheck/examples_i386/diggit-Ex.timings:

nameusersystemelapsed
aqtl-methods16.22 0.3621.34
conditional-methods17.00 0.5317.54
correlation000
diggit-class1.870.011.90
diggit-methods6.370.066.54
diggit-plot17.66 0.1617.81
fcnv-methods2.040.052.09
marina-methods103.52 6.52110.06
mutualInfo2.080.002.09

diggit.Rcheck/examples_x64/diggit-Ex.timings:

nameusersystemelapsed
aqtl-methods15.28 0.2515.53
conditional-methods18.47 0.1918.65
correlation000
diggit-class1.760.001.77
diggit-methods6.260.086.33
diggit-plot16.77 0.0916.86
fcnv-methods1.870.061.94
marina-methods100.17 7.22107.41
mutualInfo2.660.002.68