BioC 3.5: CHECK report for MetCirc on oaxaca

Package: MetCirc

Version: 1.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetCirc_1.1.4.tar.gz

StartedAt: 2017-03-04 05:39:48 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:41:21 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 92.6 seconds

RetCode: 0

Status:  OK

CheckDir: MetCirc.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetCirc_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MetCirc.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.4’
* 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 7.861  0.253   8.120
highlight            4.638  0.057   5.339
* 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	0.071	0.001	0.072
adduct-set	0.393	0.011	0.405
adduct	0.469	0.006	0.475
allocatePrecursor2mz	7.861	0.253	8.120
binning	2.010	0.300	2.311
cart2Polar	0.001	0.000	0.001
circosLegend	0.337	0.033	0.370
classes-set	0.391	0.012	0.404
classes	0.399	0.013	0.412
combine	0.741	0.013	0.755
convert2MSP	0.403	0.010	0.412
convertMSP2MSP	0.024	0.002	0.026
createLink0Matrix	0.129	0.003	0.132
createLinkMatrix	0.897	0.040	0.937
createOrderedSimMat	2.148	0.470	2.618
createSimilarityMatrix	0.046	0.004	0.050
cutLinkMatrix	0.688	0.038	0.727
cutUniquePrecursor	0.001	0.000	0.000
extract-methods	0.405	0.008	0.413
getBegEndIndMSP	0.393	0.021	0.414
getLinkMatrixIndices	0.001	0.000	0.000
getPrecursorMZ	0.431	0.023	0.455
getRT	0.387	0.020	0.407
highlight	4.638	0.057	5.339
information-set	0.369	0.019	0.387
information	0.339	0.004	0.342
length-method	0.401	0.005	0.406
minFragCart2Polar	2.107	0.064	2.171
msp2FunctionalLossesMSP	0.495	0.025	0.520
names-set	0.416	0.011	0.426
names	0.302	0.017	0.319
peaks	0.544	0.039	0.584
plotCircos	2.461	0.051	2.513
printInformationSelect	0.811	0.041	0.854
shinyCircos	0.407	0.022	0.430
show-method	0.486	0.012	0.498
thresholdLinkMatrix	0.861	0.024	0.886
truncateName	0.001	0.000	0.001