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BioC 3.6: CHECK report for GRmetrics on malbec1

This page was generated on 2017-08-16 13:24:51 -0400 (Wed, 16 Aug 2017).

Package 602/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRmetrics 1.3.3
Nicholas Clark , Mario Medvedovic
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GRmetrics
Last Changed Rev: 131647 / Revision: 131943
Last Changed Date: 2017-07-29 02:45:27 -0400 (Sat, 29 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GRmetrics
Version: 1.3.3
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GRmetrics_1.3.3.tar.gz
StartedAt: 2017-08-15 23:47:02 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:50:20 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 198.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GRmetrics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GRmetrics_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GRmetrics.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRmetrics’ version ‘1.3.3’
* 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 ‘GRmetrics’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GRcalculate: no visible binding for global variable
  ‘treatment_duration’
.GRlogisticFit: no visible binding for global variable ‘experiment’
GRdrawDRC: no visible binding for global variable ‘GRvalue’
Undefined global functions or variables:
  GRvalue experiment treatment_duration
* 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
GRbox 13.764  0.044  13.639
GRfit  7.860  0.008   7.880
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/GRmetrics.Rcheck/00check.log’
for details.


GRmetrics.Rcheck/00install.out:

* installing *source* package ‘GRmetrics’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GRmetrics)

GRmetrics.Rcheck/GRmetrics-Ex.timings:

nameusersystemelapsed
GRbox13.764 0.04413.639
GRdrawDRC2.6680.0242.693
GRfit7.8600.0087.880
GRgetDefs0.6880.0160.708
GRgetGroupVars0.6640.0000.662
GRgetMetrics0.6280.0000.630
GRgetValues0.6440.0000.648
GRscatter4.8200.0044.829