Package: RMassBank

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RMassBank.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RMassBank_2.8.0.tar.gz

StartedAt: 2018-10-15 04:43:30 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 04:46:18 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 168.2 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RMassBank.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RMassBank_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RMassBank.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RMassBank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RMassBank’ version ‘2.8.0’
* package encoding: UTF-8
* 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 ‘RMassBank’ 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findPattern: no visible global function definition for
  ‘capture.output’
.get.mol2formula: no visible global function definition for
  ‘capture.output’
.pubChemOnline: no visible global function definition for ‘URLencode’
addPeaks: no visible global function definition for ‘read.csv’
analyzeMsMs.formula.optimized: no visible binding for global variable
  ‘occurrenceMatrix’
checkIsotopes: no visible global function definition for ‘data’
checkIsotopes : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
createSpecsFromPeaklists: no visible global function definition for
  ‘read.csv’
deprofile.spline : <anonymous>: no visible global function definition
  for ‘smooth.spline’
deprofile.spline : <anonymous>: no visible global function definition
  for ‘predict’
findEIC: no visible global function definition for ‘predict’
findMsMsHRperxcms.direct : getRT : <anonymous>: no visible global
  function definition for ‘median’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘capture.output’
gatherSpectrum: no visible global function definition for
  ‘packageVersion’
getCSID: no visible global function definition for ‘URLencode’
getCactus: no visible global function definition for ‘URLencode’
getCtsKey: no visible global function definition for ‘URLencode’
getMolecule: no visible global function definition for ‘capture.output’
getPcCHEBI: no visible global function definition for ‘URLencode’
getPcIUPAC: no visible global function definition for ‘URLencode’
getPcId: no visible global function definition for ‘URLencode’
getPcInchiKey: no visible global function definition for ‘URLencode’
getPcSDF: no visible global function definition for ‘URLencode’
getPcSynonym: no visible global function definition for ‘URLencode’
loadInfolist: no visible global function definition for ‘read.csv’
loadInfolist: no visible global function definition for ‘read.csv2’
loadList: no visible global function definition for ‘read.csv’
loadList: no visible global function definition for ‘read.csv2’
makeMollist: no visible global function definition for ‘write.table’
makeRecalibration: no visible global function definition for ‘par’
mbWorkflow: no visible global function definition for ‘write.csv’
msmsRead: no visible global function definition for ‘read.csv’
msmsRead.RAW : getRT : <anonymous>: no visible global function
  definition for ‘median’
msmsRead.RAW: no visible global function definition for
  ‘capture.output’
msmsRead.ticms2: no visible global function definition for ‘read.csv’
msmsRead.ticms2: no visible global function definition for
  ‘c.msmsWSspecs’
newStep2WorkFlow: no visible global function definition for ‘read.csv’
parseMassBank: no visible binding for global variable ‘type.convert’
parseMassBank: no visible global function definition for
  ‘flush.console’
plotMbWorkspaces: no visible global function definition for ‘points’
plotRecalibration: no visible global function definition for ‘par’
plotRecalibration.direct: no visible global function definition for
  ‘predict’
plotRecalibration.direct: no visible global function definition for
  ‘lines’
plotRecalibration.direct: no visible global function definition for
  ‘heat.colors’
processProblematicPeaks: no visible global function definition for
  ‘write.csv’
progressBarHook: no visible global function definition for
  ‘txtProgressBar’
progressBarHook: no visible global function definition for
  ‘setTxtProgressBar’
recalibrate.identity: no visible global function definition for ‘lm’
recalibrate.linear: no visible global function definition for ‘lm’
recalibrate.loess: no visible global function definition for ‘loess’
recalibrate.mean: no visible global function definition for ‘lm’
recalibrateSingleSpec: no visible global function definition for
  ‘predict’
toRMB : <anonymous>: no visible global function definition for ‘median’
show,mbWorkspace: no visible global function definition for ‘str’
Undefined global functions or variables:
  URLencode c.msmsWSspecs capture.output data flush.console heat.colors
  lines lm loess median occurrenceMatrix packageVersion par points
  predict read.csv read.csv2 setTxtProgressBar smooth.spline str
  txtProgressBar type.convert write.csv write.table
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "lm", "loess", "median", "predict",
             "smooth.spline")
  importFrom("utils", "URLencode", "capture.output", "data",
             "flush.console", "packageVersion", "read.csv", "read.csv2",
             "setTxtProgressBar", "str", "txtProgressBar",
             "type.convert", "write.csv", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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-3.7-bioc/meat/RMassBank.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RMassBank
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RMassBank’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RMassBank)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #### doRUnit.R --- Run RUnit tests
> ####------------------------------------------------------------------------
> 
> ### Structure borrowed from rcppgls:
> ### https://github.com/eddelbuettel/rcppgsl/blob/master/tests/doRUnit.R
> 
> if(require("RUnit", quietly = TRUE)) {
+ 	if(require("RMassBankData", quietly = TRUE) && !(compareVersion(installed.packages()["RMassBankData","Version"],"1.99.0") == -1)) {
+ 		pkg <- "RMassBank"
+ 		print("Starting tests")
+ 		require(pkg, character.only=TRUE)
+ 
+ 		path <- system.file("unitTests", package = pkg)
+ 
+ 		stopifnot(file.exists(path), file.info(path.expand(path))$isdir)
+ 
+ 		source(file.path(path, "runTests.R"), echo = TRUE)
+ 	} else {
+ 		## Taking this message out until the new RMassBankData is on bioc, just to avoid confusion.
+         # message("Package RMassBankData with version > 1.99 not available, cannot run unit tests")
+ 	}
+ } else {
+ 	message("Package RUnit not available, cannot run unit tests")
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  1.248   0.219   1.449 

name	user	system	elapsed
CTS.externalIdSubset	0.001	0.000	0.001
CTS.externalIdTypes	0.002	0.001	0.002
RmbDefaultSettings	0.006	0.001	0.007
add.formula	0.005	0.000	0.006
addMB	0.001	0.000	0.001
addPeaks	0.001	0.000	0.001
addPeaksManually	0.001	0.000	0.001
aggregateSpectra	0.001	0.000	0.001
analyzeMsMs	0.001	0.000	0.001
annotator.default	0.001	0.000	0.001
archiveResults	0.009	0.000	0.010
cleanElnoise	0.001	0.000	0.001
combineMultiplicities	0.002	0.000	0.002
compileRecord	0.001	0.000	0.001
createMolfile	0.001	0.001	0.001
dbe	0.001	0.000	0.002
deprofile	0.002	0.000	0.002
exportMassbank	0.001	0.000	0.001
filterLowaccResults	0.001	0.000	0.001
filterMultiplicity	0.001	0.000	0.001
filterPeakSatellites	0.002	0.000	0.002
filterPeaksMultiplicity	0.002	0.000	0.002
findMass	0.895	0.087	0.323
findMsMsHR	0.001	0.000	0.001
findMsMsHRperxcms	0.001	0.000	0.001
findMz	0.001	0.000	0.002
findMz.formula	0.018	0.002	0.015
findProgress	0.001	0.000	0.001
flatten	0.001	0.000	0.001
formulastring.to.list	0.002	0.000	0.002
gatherCompound	0.001	0.000	0.001
gatherData	0.001	0.000	0.001
gatherDataBabel	0.001	0.000	0.001
gatherDataUnknown	0.001	0.000	0.001
gatherPubChem	0.001	0.000	0.001
getCSID	0.001	0.000	0.001
getCactus	0.031	0.004	0.999
getCtsKey	0.007	0.002	2.950
getCtsRecord	0.018	0.002	0.532
getMolecule	0.072	0.009	0.052
getPcId	0.014	0.002	0.352
is.valid.formula	0.002	0.000	0.002
loadInfolists	0.001	0.000	0.001
loadList	0.001	0.000	0.001
makeMollist	0.001	0.000	0.002
makeRecalibration	0.002	0.000	0.002
mbWorkflow	0.002	0.000	0.001
order.formula	0.002	0.000	0.002
parseMassBank	0.002	0.000	0.001
plotMbWorkspaces	0.000	0.000	0.001
ppm	0.001	0.000	0.002
problematicPeaks	0.001	0.000	0.001
reanalyzeFailpeaks	0.001	0.000	0.001
recalibrate	0.002	0.000	0.002
recalibrate.addMS1data	0.001	0.000	0.001
smiles2mass	0.000	0.000	0.001
to.limits.rcdk	0.003	0.000	0.002
toMassbank	0.002	0.000	0.002
toRMB	0.001	0.000	0.002
updateSettings	0.002	0.000	0.001
validate	0.002	0.000	0.002