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BioC 3.5: CHECK report for SIMAT on malbec2

This page was generated on 2017-10-18 14:16:40 -0400 (Wed, 18 Oct 2017).

Package 1222/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMAT 1.8.0
Mo R. Nezami Ranjbar
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/SIMAT
Branch: RELEASE_3_5
Last Commit: f170a4e
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: SIMAT
Version: 1.8.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SIMAT_1.8.0.tar.gz
StartedAt: 2017-10-18 02:32:37 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:33:37 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 59.6 seconds
RetCode: 0
Status:  OK 
CheckDir: SIMAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SIMAT_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SIMAT.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 ‘SIMAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIMAT’ version ‘1.8.0’
* 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 ‘SIMAT’ 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
getRIStandard: no visible global function definition for ‘read.csv’
plotEIC: no visible global function definition for ‘stack’
plotEIC: no visible global function definition for ‘dnorm’
plotEIC: no visible global function definition for ‘dev.copy’
plotEIC: no visible binding for global variable ‘pdf’
plotEIC: no visible global function definition for ‘dev.off’
plotTIC: no visible binding for global variable ‘rt’
Undefined global functions or variables:
  dev.copy dev.off dnorm pdf read.csv rt stack
Consider adding
  importFrom("grDevices", "dev.copy", "dev.off", "pdf")
  importFrom("stats", "dnorm", "rt")
  importFrom("utils", "read.csv", "stack")
to your NAMESPACE file.
* 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
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/SIMAT.Rcheck/00check.log’
for details.


SIMAT.Rcheck/00install.out:

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

SIMAT.Rcheck/SIMAT-Ex.timings:

nameusersystemelapsed
Library0.0040.0000.006
RItable0.0040.0000.001
Run0.0680.0000.070
Targets0.0000.0000.002
getEIC0.2200.0000.218
getPeak0.3280.0000.331
getPeakScore0.2880.0000.289
getRI0.0000.0000.002
getRIStandard0.0040.0000.005
getScore000
getTarget2.0040.0002.004
getTargetTable0.0040.0000.002
optFrag1.7360.0041.741
plotEIC1.8400.0001.838
plotTIC0.4040.0000.406
putTargetTable0.0040.0000.002
readCDF1.6720.0001.671