BioC 3.6: CHECK report for MetCirc on malbec1

Package: MetCirc

Version: 1.3.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MetCirc_1.3.0.tar.gz

StartedAt: 2017-08-16 00:36:43 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:38:01 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 77.5 seconds

RetCode: 0

Status:  OK

CheckDir: MetCirc.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MetCirc_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MetCirc.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 ‘MetCirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetCirc’ version ‘1.3.0’
* 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 ‘MetCirc’ 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 object imported by a ':::' call: ‘circlize:::get.sector.data’
  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 ... OK
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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
allocatePrecursor2mz 5.196   0.12    5.32
* 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-3.6-bioc/meat/MetCirc.Rcheck/00check.log’
for details.

* installing *source* package ‘MetCirc’ ...
** 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 (MetCirc)

name	user	system	elapsed
NDP	0.028	0.000	0.029
adduct-set	0.312	0.004	0.314
adduct	0.328	0.004	0.332
allocatePrecursor2mz	5.196	0.120	5.320
binning	2.052	0.144	2.196
cart2Polar	0.000	0.000	0.001
circosLegend	0.260	0.004	0.265
classes-set	0.248	0.000	0.247
classes	0.232	0.000	0.233
combine	0.480	0.000	0.481
convert2MSP	0.244	0.000	0.244
convertMSP2MSP	0.020	0.000	0.017
createLink0Matrix	0.080	0.000	0.083
createLinkMatrix	0.504	0.004	0.508
createOrderedSimMat	0.816	0.244	1.061
createSimilarityMatrix	0.048	0.000	0.048
cutLinkMatrix	0.528	0.000	0.530
cutUniquePrecursor	0.000	0.000	0.001
extract-methods	0.252	0.004	0.259
getBegEndIndMSP	0.260	0.000	0.259
getLinkMatrixIndices	0	0	0
getPrecursorMZ	0.252	0.004	0.253
getRT	0.244	0.000	0.246
highlight	3.252	0.000	3.254
information-set	0.232	0.000	0.234
information	0.248	0.000	0.247
length-method	0.232	0.004	0.235
minFragCart2Polar	1.612	0.008	1.621
msp2FunctionalLossesMSP	0.348	0.000	0.347
names-set	0.244	0.000	0.243
names	0.264	0.004	0.269
peaks	0.340	0.020	0.362
plotCircos	2.144	0.000	2.147
printInformationSelect	0.556	0.000	0.557
shinyCircos	0.276	0.000	0.276
show-method	0.264	0.000	0.267
thresholdLinkMatrix	0.520	0.004	0.526
truncateName	0	0	0