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CHECK report for RMassBank on tokay1

This page was generated on 2019-04-13 11:22:19 -0400 (Sat, 13 Apr 2019).

Package 1321/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 2.10.1
RMassBank at Eawag
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/RMassBank
Branch: RELEASE_3_8
Last Commit: b0ac42f
Last Changed Date: 2019-01-04 13:46:59 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RMassBank
Version: 2.10.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RMassBank.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RMassBank_2.10.1.tar.gz
StartedAt: 2019-04-13 05:05:28 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:09:26 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 237.9 seconds
RetCode: 0
Status:  OK  
CheckDir: RMassBank.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RMassBank.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RMassBank_2.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RMassBank.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RMassBank/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RMassBank' version '2.10.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/RMassBank.Rcheck/00check.log'
for details.



Installation output

RMassBank.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RMassBank_2.10.1.tar.gz && rm -rf RMassBank.buildbin-libdir && mkdir RMassBank.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RMassBank.buildbin-libdir RMassBank_2.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RMassBank_2.10.1.zip && rm RMassBank_2.10.1.tar.gz RMassBank_2.10.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  297k  100  297k    0     0  7428k      0 --:--:-- --:--:-- --:--:-- 8260k

install for i386

* installing *source* package 'RMassBank' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RMassBank'
    finding HTML links ... done
    CTS.externalIdSubset                    html  
    CTS.externalIdTypes                     html  
    RmbDefaultSettings                      html  
    RmbSettings                             html  
    add.formula                             html  
    addMB                                   html  
    addPeaks                                html  
    addPeaksManually                        html  
    addProperty                             html  
    aggregateSpectra                        html  
    analyzeMsMs                             html  
    annotator.default                       html  
    archiveResults                          html  
    checkIsotopes                           html  
    checkSpectra                            html  
    cleanElnoise                            html  
    combineMultiplicities                   html  
    compileRecord                           html  
    createMolfile                           html  
    dbe                                     html  
    deprofile                               html  
    exportMassbank                          html  
    filterLowaccResults                     html  
    filterMultiplicity                      html  
    filterPeakSatellites                    html  
    filterPeaksMultiplicity                 html  
    findEIC                                 html  
    findMass                                html  
    findMsMsHR                              html  
    findMsMsHR.direct                       html  
    findMsMsHR.ticms2                       html  
    findMsMsHRperxcms                       html  
    findMz                                  html  
    findMz.formula                          html  
    findProgress                            html  
    flatten                                 html  
    formulastring.to.list                   html  
    gatherCompound                          html  
    gatherData                              html  
    gatherDataBabel                         html  
    gatherDataUnknown                       html  
    gatherPubChem                           html  
    getCSID                                 html  
    getCactus                               html  
    getCtsKey                               html  
    getCtsRecord                            html  
    getData                                 html  
    getMolecule                             html  
    finding level-2 HTML links ... done

    getPcId                                 html  
    is.valid.formula                        html  
    loadInfolists                           html  
    loadList                                html  
    makeMollist                             html  
    makePeaksCache                          html  
    makeRecalibration                       html  
    mbWorkflow                              html  
    mbWorkspace-class                       html  
    msmsRead.RAW                            html  
    msmsRead                                html  
    msmsWorkflow                            html  
    msmsWorkspace-class                     html  
    newMbWorkspace                          html  
    newMsmsWorkspace                        html  
    order.formula                           html  
    parseMassBank                           html  
    peaksMatched                            html  
    peaksUnmatched                          html  
    plotMbWorkspaces                        html  
    plotRecalibration                       html  
    ppm                                     html  
    problematicPeaks                        html  
    processProblematicPeaks                 html  
    progressBarHook                         html  
    reanalyzeFailpeaks                      html  
    recalibrate                             html  
    recalibrate.addMS1data                  html  
    selectPeaks                             html  
    selectSpectra                           html  
    setData                                 html  
    smiles2mass                             html  
    spectraCount                            html  
    to.limits.rcdk                          html  
    toMassbank                              html  
    toRMB                                   html  
    updateSettings                          html  
    validate                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RMassBank' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RMassBank' as RMassBank_2.10.1.zip
* DONE (RMassBank)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RMassBank' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

RMassBank.Rcheck/tests_i386/doRUnit.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   1.09    0.56    1.67 

RMassBank.Rcheck/tests_x64/doRUnit.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   1.17    0.48    1.70 

Example timings

RMassBank.Rcheck/examples_i386/RMassBank-Ex.timings

nameusersystemelapsed
CTS.externalIdSubset000
CTS.externalIdTypes000
RmbDefaultSettings0.000.000.02
add.formula000
addMB000
addPeaks0.020.000.01
addPeaksManually000
aggregateSpectra000
analyzeMsMs000
annotator.default000
archiveResults000
cleanElnoise000
combineMultiplicities000
compileRecord000
createMolfile000
dbe000
deprofile000
exportMassbank000
filterLowaccResults000
filterMultiplicity000
filterPeakSatellites000
filterPeaksMultiplicity000
findMass0.350.030.28
findMsMsHR000
findMsMsHRperxcms000
findMz000
findMz.formula0.020.000.02
findProgress000
flatten000
formulastring.to.list000
gatherCompound000
gatherData000
gatherDataBabel000
gatherDataUnknown000
gatherPubChem000
getCSID000
getCactus0.110.040.84
getCtsKey0.680.372.00
getCtsRecord0.070.001.15
getMolecule0.010.000.02
getPcId0.020.000.36
is.valid.formula000
loadInfolists000
loadList000
makeMollist000
makeRecalibration000
mbWorkflow000
order.formula000
parseMassBank000
plotMbWorkspaces000
ppm000
problematicPeaks000
reanalyzeFailpeaks000
recalibrate000
recalibrate.addMS1data000
smiles2mass000
to.limits.rcdk000
toMassbank000
toRMB000
updateSettings000
validate000

RMassBank.Rcheck/examples_x64/RMassBank-Ex.timings

nameusersystemelapsed
CTS.externalIdSubset000
CTS.externalIdTypes000
RmbDefaultSettings0.010.000.02
add.formula000
addMB000
addPeaks000
addPeaksManually000
aggregateSpectra000
analyzeMsMs000
annotator.default000
archiveResults0.020.000.01
cleanElnoise000
combineMultiplicities000
compileRecord000
createMolfile000
dbe000
deprofile000
exportMassbank000
filterLowaccResults000
filterMultiplicity000
filterPeakSatellites000
filterPeaksMultiplicity000
findMass0.520.070.25
findMsMsHR000
findMsMsHRperxcms000
findMz000
findMz.formula000
findProgress000
flatten000
formulastring.to.list000
gatherCompound000
gatherData000
gatherDataBabel000
gatherDataUnknown000
gatherPubChem000
getCSID000
getCactus0.060.000.77
getCtsKey0.660.221.58
getCtsRecord0.030.000.79
getMolecule0.090.000.04
getPcId0.020.000.35
is.valid.formula000
loadInfolists000
loadList000
makeMollist000
makeRecalibration000
mbWorkflow000
order.formula000
parseMassBank000
plotMbWorkspaces000
ppm000
problematicPeaks000
reanalyzeFailpeaks000
recalibrate000
recalibrate.addMS1data000
smiles2mass000
to.limits.rcdk000
toMassbank000
toRMB000
updateSettings000
validate000