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BioC 3.5: CHECK report for bigmelon on toluca2

This page was generated on 2017-04-23 14:42:09 -0400 (Sun, 23 Apr 2017).

Package 107/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigmelon 1.1.15
Tyler J. Gorrie-Stone
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bigmelon
Last Changed Rev: 128460 / Revision: 129046
Last Changed Date: 2017-04-10 08:44:20 -0400 (Mon, 10 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bigmelon
Version: 1.1.15
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmelon_1.1.15.tar.gz
StartedAt: 2017-04-23 00:52:47 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 00:59:09 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 382.3 seconds
RetCode: 0
Status:  OK 
CheckDir: bigmelon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmelon_1.1.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/bigmelon.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bigmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigmelon’ version ‘1.1.15’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bigmelon’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘minfi:::pickCompProbes’ ‘minfi:::projectCellType’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
es2gds: no visible global function definition for ‘colData’
estimateCellCounts.gds: no visible global function definition for
  ‘colData’
Undefined global functions or variables:
  colData
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
iadd 45.794  1.798  47.713
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/bigmelon.Rcheck/00check.log’
for details.


bigmelon.Rcheck/00install.out:

* installing *source* package ‘bigmelon’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘fot’ in package ‘bigmelon’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bigmelon)

bigmelon.Rcheck/bigmelon-Ex.timings:

nameusersystemelapsed
GEOtoGDS0.0010.0000.001
app2gds1.2180.0351.261
backupGdsn0.4350.0460.486
bigmelon-accessors2.9360.6543.596
bigmelon-internal0.2170.0150.234
bigmelon-normalization2.1530.2712.432
combogds0.3990.0320.433
es2gds0.2140.0180.236
finalreport2gds0.0010.0000.000
gds2mlumi0.6890.0200.712
getquantilesandranks0.5050.0350.546
iadd45.794 1.79847.713
pfiltergds0.3640.0310.398
prcompgdsn0.1950.0200.217
pwodgdsn0.4980.0260.525
rankednorm0.1940.0200.216
redirect0.2190.0240.244