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BioC 3.5: CHECK report for bigmelon on malbec2

This page was generated on 2017-10-18 14:18:04 -0400 (Wed, 18 Oct 2017).

Package 108/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigmelon 1.2.0
Tyler J. Gorrie-Stone
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/bigmelon
Branch: RELEASE_3_5
Last Commit: 8b711d8
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 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
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: 1.2.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bigmelon_1.2.0.tar.gz
StartedAt: 2017-10-17 21:30:09 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 21:35:28 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 319.1 seconds
RetCode: 0
Status:  OK 
CheckDir: bigmelon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bigmelon_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/bigmelon.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 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 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 37.912   0.16  38.813
* 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
  ‘/home/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
GEOtoGDS000
app2gds1.1920.0281.273
backupGdsn0.4200.0080.429
bigmelon-accessors1.2440.2681.515
bigmelon-internal0.2720.0200.295
bigmelon-normalization2.4120.0442.460
combogds0.3440.0000.346
es2gds0.1840.0000.188
finalreport2gds0.0000.0000.001
gds2mlumi0.5640.0040.570
getquantilesandranks0.3920.0040.398
iadd37.912 0.16038.813
pfiltergds0.2720.0120.287
prcompgdsn0.1920.0000.195
pwodgdsn0.4480.0080.460
rankednorm0.1840.0000.185
redirect0.1800.0080.188