Package: RMassBank

Version: 2.15.3

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_2.15.3.tar.gz

StartedAt: 2020-01-16 08:16:08 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:20:33 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 264.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RMassBank.Rcheck

Warnings: 1

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### Running command:
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###   /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_2.15.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RMassBank.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.15.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: no visible binding for global variable ‘msmsPeaks’
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’
getCompTox: no visible global function definition for ‘URLencode’
getCtsKey: no visible global function definition for ‘URLencode’
getMolecule: no visible global function definition for ‘capture.output’
getMonoisotopicMass: no visible global function definition for ‘data’
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’
reanalyzeFailpeak: no visible binding for global variable ‘mass.calc’
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 mass.calc median msmsPeaks 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 ... WARNING
Undocumented code objects:
  ‘findMsMsHRperMsp’ ‘findMsMsHRperMsp.direct’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/RMassBank.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RMassBank
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘RMassBank’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RMassBank)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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 
  2.120   0.578   2.649 

name	user	system	elapsed
CTS.externalIdSubset	0.000	0.000	0.001
CTS.externalIdTypes	0.001	0.001	0.000
RmbDefaultSettings	0.007	0.002	0.010
add.formula	0.006	0.001	0.007
addMB	0.000	0.000	0.001
addPeaks	0.000	0.000	0.001
addPeaksManually	0	0	0
aggregateSpectra	0.001	0.000	0.001
analyzeMsMs	0.000	0.001	0.000
annotator.default	0.001	0.000	0.000
archiveResults	0.010	0.001	0.011
cleanElnoise	0	0	0
combineMultiplicities	0.001	0.001	0.001
compileRecord	0.001	0.001	0.001
createMolfile	0	0	0
dbe	0	0	0
deprofile	0	0	0
exportMassbank	0.001	0.000	0.001
filterLowaccResults	0.000	0.000	0.001
filterMultiplicity	0.000	0.001	0.001
filterPeakSatellites	0.000	0.000	0.001
filterPeaksMultiplicity	0.000	0.000	0.001
findMass	1.181	0.367	0.611
findMsMsHR	0.001	0.002	0.001
findMsMsHRperxcms	0.000	0.001	0.000
findMz	0.000	0.001	0.000
findMz.formula	0.151	0.019	0.088
findProgress	0.000	0.001	0.001
flatten	0.000	0.001	0.001
formulastring.to.list	0.002	0.001	0.003
gatherCompound	0.000	0.001	0.001
gatherData	0.001	0.001	0.000
gatherDataBabel	0.000	0.001	0.001
gatherDataUnknown	0	0	0
gatherPubChem	0.000	0.000	0.001
getCSID	0	0	0
getCactus	0.115	0.016	1.337
getCtsKey	0.019	0.004	1.689
getCtsRecord	0.027	0.006	1.383
getMolecule	0.098	0.019	0.070
getPcId	0.017	0.004	1.017
is.valid.formula	0.002	0.001	0.002
loadInfolists	0.000	0.001	0.000
loadList	0.000	0.000	0.001
makeMollist	0.000	0.001	0.001
makeRecalibration	0.000	0.001	0.000
mbWorkflow	0.001	0.000	0.001
order.formula	0.003	0.000	0.002
parseMassBank	0	0	0
plotMbWorkspaces	0.000	0.001	0.001
ppm	0.001	0.000	0.001
problematicPeaks	0.000	0.000	0.001
reanalyzeFailpeaks	0	0	0
recalibrate	0.000	0.000	0.001
recalibrate.addMS1data	0.000	0.001	0.001
smiles2mass	0	0	0
to.limits.rcdk	0.002	0.001	0.002
toMassbank	0.000	0.000	0.001
toRMB	0.000	0.000	0.001
updateSettings	0.001	0.000	0.001
validate	0.000	0.000	0.001