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BioC 3.2: CHECK report for shinyMethyl on moscato1

This page was generated on 2016-04-23 10:20:28 -0700 (Sat, 23 Apr 2016).

Package 965/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
shinyMethyl 1.4.0
Jean-Philippe Fortin
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/shinyMethyl
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: shinyMethyl
Version: 1.4.0
Command: rm -rf shinyMethyl.buildbin-libdir shinyMethyl.Rcheck && mkdir shinyMethyl.buildbin-libdir shinyMethyl.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=shinyMethyl.buildbin-libdir shinyMethyl_1.4.0.tar.gz >shinyMethyl.Rcheck\00install.out 2>&1 && cp shinyMethyl.Rcheck\00install.out shinyMethyl-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=shinyMethyl.buildbin-libdir --install="check:shinyMethyl-install.out" --force-multiarch --no-vignettes --timings shinyMethyl_1.4.0.tar.gz
StartedAt: 2016-04-23 07:26:21 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 07:38:50 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 749.1 seconds
RetCode: 0
Status:  OK  
CheckDir: shinyMethyl.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf shinyMethyl.buildbin-libdir shinyMethyl.Rcheck && mkdir shinyMethyl.buildbin-libdir shinyMethyl.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=shinyMethyl.buildbin-libdir shinyMethyl_1.4.0.tar.gz >shinyMethyl.Rcheck\00install.out 2>&1 && cp shinyMethyl.Rcheck\00install.out shinyMethyl-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=shinyMethyl.buildbin-libdir --install="check:shinyMethyl-install.out" --force-multiarch --no-vignettes --timings shinyMethyl_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/shinyMethyl.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'shinyMethyl/DESCRIPTION' ... OK
* this is package 'shinyMethyl' version '1.4.0'
* 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 whether package 'shinyMethyl' 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 ... OK
* 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [65s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
shinySummarize-methods 44.61   1.55   46.93
** running examples for arch 'x64' ... [69s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
shinySummarize-methods 50.82   1.56   52.38
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [74s]
 [75s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [74s]
 [74s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/shinyMethyl.Rcheck/00check.log'
for details.


shinyMethyl.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'shinyMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'shinyMethyl' as shinyMethyl_1.4.0.zip
* DONE (shinyMethyl)

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

nameusersystemelapsed
runShinyMethyl000
shinyMethylSet-class000
shinySummarize-methods44.61 1.5546.93

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

nameusersystemelapsed
runShinyMethyl000
shinyMethylSet-class000
shinySummarize-methods50.82 1.5652.38