BioC 3.5: CHECK report for MetCirc on veracruz2

Package: MetCirc

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetCirc_1.2.0.tar.gz

StartedAt: 2017-10-18 05:56:50 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:58:31 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 100.9 seconds

RetCode: 0

Status:  OK

CheckDir: MetCirc.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetCirc_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MetCirc.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 ‘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 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
allocatePrecursor2mz 7.726  0.297   8.265
* 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
  ‘/Users/biocbuild/bbs-3.5-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	0.082	0.002	0.087
adduct-set	0.323	0.010	0.339
adduct	0.471	0.010	0.490
allocatePrecursor2mz	7.726	0.297	8.265
binning	2.077	0.391	2.536
cart2Polar	0	0	0
circosLegend	0.327	0.011	0.348
classes-set	0.328	0.003	0.337
classes	0.318	0.003	0.330
combine	0.631	0.005	0.654
convert2MSP	0.333	0.003	0.340
convertMSP2MSP	0.021	0.001	0.023
createLink0Matrix	0.128	0.002	0.131
createLinkMatrix	0.756	0.015	0.801
createOrderedSimMat	2.451	0.615	3.154
createSimilarityMatrix	0.068	0.007	0.076
cutLinkMatrix	0.735	0.023	0.791
cutUniquePrecursor	0.001	0.000	0.001
extract-methods	0.292	0.003	0.303
getBegEndIndMSP	0.300	0.006	0.314
getLinkMatrixIndices	0.001	0.000	0.001
getPrecursorMZ	0.308	0.004	0.322
getRT	0.336	0.010	0.354
highlight	4.194	0.035	4.356
information-set	0.349	0.007	0.370
information	0.288	0.003	0.297
length-method	0.319	0.002	0.328
minFragCart2Polar	2.264	0.020	2.335
msp2FunctionalLossesMSP	0.450	0.015	0.472
names-set	0.289	0.007	0.301
names	0.303	0.003	0.312
peaks	0.543	0.048	0.609
plotCircos	2.676	0.027	2.769
printInformationSelect	0.663	0.020	0.719
shinyCircos	0.314	0.014	0.338
show-method	0.310	0.002	0.317
thresholdLinkMatrix	0.693	0.025	0.741
truncateName	0.001	0.000	0.001