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CHECK report for RMassBank on merida2

This page was generated on 2019-04-03 12:31:58 -0400 (Wed, 03 Apr 2019).

Package 1357/1696HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 2.11.1
RMassBank at Eawag
Snapshot Date: 2019-04-02 17:01:51 -0400 (Tue, 02 Apr 2019)
URL: https://git.bioconductor.org/packages/RMassBank
Branch: master
Last Commit: 2780364
Last Changed Date: 2019-01-04 13:46:55 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: RMassBank
Version: 2.11.1
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_2.11.1.tar.gz
StartedAt: 2019-04-03 03:24:06 -0400 (Wed, 03 Apr 2019)
EndedAt: 2019-04-03 03:26:57 -0400 (Wed, 03 Apr 2019)
EllapsedTime: 171.5 seconds
RetCode: 0
Status:  OK 
CheckDir: RMassBank.Rcheck
Warnings: 0

Command output

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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_2.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RMassBank.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘2.11.1’
* 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 : <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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/RMassBank.Rcheck/00check.log’
for details.



Installation output

RMassBank.Rcheck/00install.out

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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/3.6/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)

Tests output

RMassBank.Rcheck/tests/doRUnit.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 
  1.579   0.295   1.852 

Example timings

RMassBank.Rcheck/RMassBank-Ex.timings

nameusersystemelapsed
CTS.externalIdSubset000
CTS.externalIdTypes0.0000.0000.001
RmbDefaultSettings0.0060.0010.007
add.formula0.0050.0000.005
addMB000
addPeaks000
addPeaksManually000
aggregateSpectra000
analyzeMsMs000
annotator.default000
archiveResults0.0090.0000.010
cleanElnoise000
combineMultiplicities000
compileRecord000
createMolfile0.0010.0000.000
dbe0.0010.0000.000
deprofile0.0000.0000.001
exportMassbank0.0000.0000.001
filterLowaccResults000
filterMultiplicity000
filterPeakSatellites0.0000.0000.001
filterPeaksMultiplicity0.0000.0000.001
findMass0.9020.0870.357
findMsMsHR000
findMsMsHRperxcms0.0010.0000.001
findMz0.0010.0000.000
findMz.formula0.0240.0020.020
findProgress000
flatten000
formulastring.to.list0.0010.0000.002
gatherCompound0.0010.0000.001
gatherData0.0010.0000.000
gatherDataBabel0.0010.0010.000
gatherDataUnknown0.0010.0000.000
gatherPubChem000
getCSID0.0000.0000.001
getCactus0.0980.0163.185
getCtsKey0.0170.0021.201
getCtsRecord0.0260.0040.542
getMolecule0.0710.0090.049
getPcId0.0140.0020.349
is.valid.formula0.0010.0000.001
loadInfolists0.0000.0010.000
loadList000
makeMollist000
makeRecalibration0.0000.0000.001
mbWorkflow000
order.formula0.0020.0000.002
parseMassBank0.0010.0000.000
plotMbWorkspaces000
ppm000
problematicPeaks0.0000.0000.001
reanalyzeFailpeaks000
recalibrate0.0000.0000.001
recalibrate.addMS1data000
smiles2mass0.0000.0000.001
to.limits.rcdk0.0030.0010.002
toMassbank0.0000.0000.001
toRMB0.0000.0000.001
updateSettings000
validate000