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BioC 3.2: CHECK report for shinyMethyl on zin1

This page was generated on 2015-08-24 10:50:00 -0700 (Mon, 24 Aug 2015).

Package 937/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
shinyMethyl 1.3.0
Jean-Philippe Fortin
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: shinyMethyl
Version: 1.3.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings shinyMethyl_1.3.0.tar.gz
StartedAt: 2015-08-24 03:45:09 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 03:49:48 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 279.5 seconds
RetCode: 0
Status:  OK 
CheckDir: shinyMethyl.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings shinyMethyl_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/shinyMethyl.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘shinyMethyl/DESCRIPTION’ ... OK
* this is package ‘shinyMethyl’ version ‘1.3.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘shinyMethyl’ can be installed ... [19s/19s] 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 ... OK
* 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 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
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘mouse.click.indices’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘colorSet’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘genderCutoff’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘current.control.type’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘current.probe.type’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘current.density.type’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘current.control.type’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘mouse.click.indices’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘current.probe.type’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘current.density.type’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘genderCutoff’
ui.shinyMethyl: no visible binding for '<<-' assignment to
  ‘sampleColors’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/44s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
shinySummarize-methods 31.537  2.738  34.549
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [44s/45s]
 [45s/45s] OK
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/shinyMethyl.Rcheck/00check.log’
for details.


shinyMethyl.Rcheck/00install.out:

* installing *source* package ‘shinyMethyl’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (shinyMethyl)

shinyMethyl.Rcheck/shinyMethyl-Ex.timings:

nameusersystemelapsed
runShinyMethyl0.0000.0000.001
shinyMethylSet-class0.0010.0000.001
shinySummarize-methods31.537 2.73834.549