BioC 3.4: CHECK report for MetCirc on zin1

Package: MetCirc

Version: 0.99.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MetCirc_0.99.4.tar.gz

StartedAt: 2016-09-20 09:09:35 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:10:53 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 77.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MetCirc.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MetCirc_0.99.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MetCirc.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘0.99.4’
* 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 ... 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 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 6.088  0.116   6.202
* 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	0.028	0.000	0.026
allocatePrecursor2mz	6.088	0.116	6.202
binning	1.992	0.208	2.201
cart2Polar	0	0	0
circosLegend	1.220	0.000	1.222
combine	0.584	0.000	0.586
convert2MSP	0.284	0.000	0.282
createLink0Matrix	0.120	0.004	0.125
createLinkMatrix	0.948	0.004	0.953
createOrderedSimMat	1.208	0.296	1.503
createSimilarityMatrix	0.104	0.008	0.111
cutLinkMatrix	0.960	0.004	0.964
cutUniquePreMZ	0	0	0
extract-methods	0.304	0.000	0.301
getBegEndIndMSP	0.292	0.004	0.298
getLinkMatrixIndices	0	0	0
getMSP	0.416	0.024	0.439
getMetaboliteClass	0.308	0.004	0.310
getMetaboliteName	0.288	0.000	0.288
getName	0.304	0.000	0.306
getPrecursorMZ	0.344	0.000	0.347
getRT	0.292	0.000	0.294
highlight	2.676	0.000	2.675
length-method	0.292	0.000	0.293
minFragCart2Polar	1.944	0.000	1.943
msp2FunctionalLossesMSP	0.428	0.004	0.432
plotCircos	2.568	0.004	2.579
printInformationHover	1.020	0.000	1.017
setMetaboliteClass	0.296	0.000	0.297
setMetaboliteName	0.300	0.000	0.308
setName	0.300	0.000	0.301
shinyCircos	0.736	0.000	0.735
show-method	0.296	0.004	0.302
thresholdLinkMatrix	0.98	0.00	0.98
truncateName	0.000	0.000	0.001