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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:19 -0400 (Sat, 13 Apr 2019).
| Package 1321/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RMassBank 2.10.1 RMassBank at Eawag
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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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
###
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* 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.
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
###
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% 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
|
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
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RMassBank.Rcheck/examples_i386/RMassBank-Ex.timings
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RMassBank.Rcheck/examples_x64/RMassBank-Ex.timings
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