BioC 3.4: CHECK report for MetCirc on malbec1

Package: MetCirc

Version: 1.0.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MetCirc_1.0.1.tar.gz

StartedAt: 2017-04-14 23:46:15 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:47:40 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 85.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MetCirc.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MetCirc_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MetCirc.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.1’
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                            old_size new_size compress
  binnedMSP.RData               34Kb     20Kb    bzip2
  idMSMStissueproject.RData    141Kb     88Kb       xz
  idMSMStoMSP.RData             57Kb     19Kb       xz
  sd01_outputXCMS.RData        1.4Mb    1.0Mb       xz
  sd02_deconvoluted.RData       51Kb     46Kb       xz
  similarityMat.RData          516Kb    221Kb       xz
* 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 5.756  0.108    5.87
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-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	0.036	0.000	0.035
allocatePrecursor2mz	5.756	0.108	5.870
binning	2.008	0.180	2.191
cart2Polar	0	0	0
circosLegend	0.584	0.000	0.586
combine	0.608	0.000	0.606
convert2MSP	0.292	0.000	0.294
createLink0Matrix	0.112	0.000	0.113
createLinkMatrix	0.784	0.000	0.786
createOrderedSimMat	0.900	0.176	1.077
createSimilarityMatrix	0.072	0.004	0.078
cutLinkMatrix	0.716	0.000	0.716
cutUniquePreMZ	0.000	0.004	0.000
extract-methods	0.268	0.000	0.269
getBegEndIndMSP	0.272	0.000	0.271
getLinkMatrixIndices	0	0	0
getMSP	0.348	0.040	0.386
getMetaboliteClass	0.288	0.004	0.293
getMetaboliteName	0.300	0.000	0.301
getName	0.280	0.000	0.282
getPrecursorMZ	0.336	0.000	0.337
getRT	0.292	0.000	0.294
highlight	2.504	0.000	2.506
length-method	0.364	0.004	0.371
minFragCart2Polar	1.764	0.000	1.763
msp2FunctionalLossesMSP	0.384	0.000	0.384
plotCircos	2.476	0.000	2.479
printInformationHover	1.140	0.000	1.142
setMetaboliteClass	0.32	0.00	0.32
setMetaboliteName	0.272	0.000	0.272
setName	0.316	0.000	0.318
shinyCircos	0.652	0.000	0.655
show-method	0.256	0.000	0.260
thresholdLinkMatrix	0.724	0.000	0.728
truncateName	0	0	0