Thomas N. Lawson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/msPurity |
| Branch: RELEASE_3_9 |
| Last Commit: e5cd054 |
| Last Changed Date: 2019-05-02 11:54:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:58:03 -0400 (Wed, 16 Oct 2019).
| Package 1057/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| msPurity 1.10.0 Thomas N. Lawson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: msPurity |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.10.0.tar.gz |
| StartedAt: 2019-10-16 04:53:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:08:09 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 861.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: msPurity.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.10.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/msPurity.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msPurity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msPurity’ version ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
.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 ‘msPurity’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.8Mb
sub-directories of 1Mb or more:
extdata 11.1Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘dbplyr’
All declared Imports should be used.
Package in Depends field not imported from: ‘Rcpp’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Missing or unexported object: ‘stats::mean’
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CV: no visible global function definition for ‘sd’
Getfiles: no visible global function definition for ‘fix’
assessPuritySingle: no visible binding for global variable ‘parallel’
averageCluster: no visible global function definition for ‘sd’
averageCluster: no visible global function definition for ‘median’
covar: no visible global function definition for ‘sd’
custom_dbWriteTable: no visible global function definition for ‘head’
dimsPredictPuritySingle: no visible global function definition for
‘read.csv’
dimsPredictPuritySingleMz: no visible global function definition for
‘png’
dimsPredictPuritySingleMz: no visible binding for global variable
‘mtchi’
dimsPredictPuritySingleMz: no visible binding for global variable
‘alli’
dimsPredictPuritySingleMz: no visible global function definition for
‘points’
dimsPredictPuritySingleMz: no visible binding for global variable
‘mtch’
dimsPredictPuritySingleMz: no visible global function definition for
‘text’
dimsPredictPuritySingleMz: no visible global function definition for
‘dev.off’
dimsPredictPuritySingleMz: no visible global function definition for
‘median’
dimsPredictPuritySingleMz: no visible global function definition for
‘sd’
export2sqlite: no visible global function definition for
‘packageVersion’
filterPrecursors: no visible binding for global variable
‘l_speakmetaFiltered’
filterSMeta: no visible binding for global variable ‘accession’
filterSMeta: no visible binding for global variable ‘inPurity’
filterSMeta: no visible global function definition for ‘lower’
filterSMeta: no visible binding for global variable ‘polarity’
filterSMeta: no visible binding for global variable ‘instrument_type’
filterSMeta: no visible binding for global variable ‘instrument’
filterSMeta: no visible binding for global variable ‘name.y’
filterSMeta: no visible binding for global variable ‘retention_time’
filterSMeta: no visible binding for global variable ‘grpid’
filterSMeta: no visible binding for global variable ‘pid’
filterSMeta: no visible binding for global variable ‘spectrum_type’
flag_remove: no visible global function definition for ‘write.csv’
getScanPeaksSqlite: no visible binding for global variable ‘pid’
getScanPeaksSqlite: no visible binding for global variable
‘library_spectra_meta_id’
getScanPeaksSqlite: no visible binding for global variable ‘pass_flag’
getScanPeaksSqlite: no visible binding for global variable ‘type’
getScanPeaksSqlite: no visible binding for global variable
‘spectraType’
getScanPeaksSqlite: no visible binding for global variable ‘ra’
getSmeta: no visible binding for global variable ‘pid’
getXcmsSmSummary: no visible binding for global variable ‘q_con’
get_topn: no visible binding for global variable ‘topn’
getxcmsSetObject: no visible global function definition for
‘sampclass<-’
groupPeaksEx: no visible binding for global variable ‘median’
iwNormGauss: no visible global function definition for ‘dnorm’
iwNormGauss: no visible global function definition for ‘approxfun’
iwNormQE.5: no visible global function definition for ‘approxfun’
iwNormRcosine: no visible global function definition for ‘approxfun’
linearPurity: no visible global function definition for ‘approxfun’
matchi: no visible global function definition for ‘match_factor’
medGroup: no visible binding for global variable ‘median’
median_match_results: no visible global function definition for
‘median’
msfrProcess: no visible global function definition for ‘read.csv’
plotPurity: no visible global function definition for ‘png’
plotPurity: no visible binding for global variable ‘idx’
plotPurity: no visible binding for global variable ‘purity’
plotPurity: no visible binding for global variable ‘variable’
plotPurity: no visible global function definition for ‘dev.off’
plotPurity: no visible global function definition for ‘write.csv’
pp4file: no visible global function definition for ‘png’
pp4file: no visible global function definition for ‘plot’
pp4file: no visible global function definition for ‘lines’
pp4file: no visible global function definition for ‘legend’
pp4file: no visible global function definition for ‘abline’
pp4file: no visible global function definition for ‘dev.off’
pp4file: no visible global function definition for ‘median’
predictPurityLCMSloop: no visible global function definition for
‘median’
predictPurityLCMSloop : : no visible global function
definition for ‘na.omit’
predictPurityLCMSloop : : no visible global function
definition for ‘median’
predictPurityLCMSloop : : no visible global function
definition for ‘sd’
purityA: no visible binding for global variable ‘i’
queryVlibrary: no visible binding for global variable ‘precursor_mz’
queryVlibrary: no visible binding for global variable ‘retention_time’
queryVlibrarySingle: no visible binding for global variable ‘pid’
queryVlibrarySingle: no visible binding for global variable
‘library_spectra_meta_id’
removeIsotopes: no visible global function definition for ‘write.csv’
rsd: no visible global function definition for ‘sd’
rsde: no visible global function definition for ‘sd’
setFlagMatrix: no visible global function definition for ‘median’
set_snr_ra: no visible global function definition for ‘median’
snrFilter: no visible global function definition for ‘median’
stde: no visible global function definition for ‘sd’
stderror: no visible global function definition for ‘sd’
sum_calc_peaklist: no visible binding for global variable ‘median’
write_msp_single: no visible global function definition for
‘packageVersion’
xcmsGroupPurity: no visible binding for global variable ‘median’
xcmsGroupPurity: no visible global function definition for ‘median’
averageSpectra,purityD: no visible binding for global variable ‘i’
subtract,purityD: no visible binding for global variable ‘i’
validate,purityA: no visible global function definition for ‘head’
writeOut,purityD: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
abline accession alli approxfun dev.off dnorm fix grpid head i idx
inPurity instrument instrument_type l_speakmetaFiltered legend
library_spectra_meta_id lines lower match_factor median mtch mtchi
na.omit name.y packageVersion parallel pass_flag pid plot png points
polarity precursor_mz purity q_con ra read.csv retention_time
sampclass<- sd spectraType spectrum_type text topn type variable
write.csv
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "abline", "legend", "lines", "plot", "points",
"text")
importFrom("stats", "approxfun", "dnorm", "median", "na.omit", "sd")
importFrom("utils", "fix", "head", "packageVersion", "read.csv",
"write.csv")
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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
frag4feature-purityA-method 75.892 7.407 76.627
dimsPredictPurity-purityD-method 68.734 4.718 74.656
flag_remove 36.336 13.668 26.996
purityX 22.734 8.391 20.958
assessPuritySingle 19.683 0.213 19.939
purityA 17.586 0.255 17.827
groupPeaks-purityD-method 13.694 3.284 16.988
subtract-purityD-method 13.047 3.899 16.946
createDatabase 13.967 1.253 15.257
groupPeaksEx 11.172 3.326 14.499
averageSpectra-purityD-method 10.107 3.576 13.720
combineAnnotations 13.309 0.230 16.207
filterp-purityD-method 10.010 3.207 13.571
spectralMatching 5.284 3.133 10.247
averageSpectraSingle 4.837 1.683 6.525
averageIntraFragSpectra-purityA-method 5.154 0.032 5.215
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/msPurity.Rcheck/00check.log’
for details.
msPurity.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msPurity ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘msPurity’ ... ** 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 (msPurity)
msPurity.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> library(testthat)
> library(msPurity)
Loading required package: Rcpp
> Sys.setenv("R_TESTS" = "")
> test_check("msPurity")
[1] "\n"
[1] "########################################################"
[1] "## Checking pcalc functions ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking purityA ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking frag4feature ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking filterFragSpectra ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageIntraFragSpectra ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageInterFragSpectra ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageAllFragSpectra ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageIntraFragSpectra (with filter) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageInterFragSpectra (with filter) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageAllFragSpectra (with filter) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking createMSP functions ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## checking flag and remove (lc-ms) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking database (old schema) ##"
[1] "########################################################"
[1] "\n"
[1] "#######################################################"
[1] "## Checking database (new schema) ##"
[1] "#######################################################"
[1] "\n"
[1] "########################################################"
[1] "## Testing spectral matching (spectralMatching) qvl ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Testing spectral matching (spectralMatching) lvl ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Testing spectral matching (spectralMatching) qvq ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking combine annotations based functions ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking purityX (grouped) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking purityX (single file) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking file list function ##"
[1] "########################################################"
[1] "=== check for using csv ==="
[1] "=== check for using mzML ==="
[1] "########################################################"
[1] "## Check average spectra (function only) ##"
[1] "########################################################"
[1] "=== check single core ==="
[1] "=== check simple clustering ==="
[1] "=== check using MsFileReader output (median SNR thres) ==="
snmeth: median[1] "=== check using MsFileReader output (precalc SNR thres) ==="
snmeth: precalc[1] "########################################################"
[1] "## Check mz subtraction (function only) ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Check predict purity (function only) ##"
[1] "########################################################"
[1] "=== Check predicted purity for mzML files ==="
[1] "########################################################"
[1] "## Check groupPeaks (function only) ##"
[1] "########################################################"
[1] "=== check single core ==="
[1] "########################################################"
[1] "## Check mzML Workflow ##"
[1] "########################################################"
[1] "averaging spectra"
[1] "filtering spectra"
[1] "subtracting"
[1] "purity prediction"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 175 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
274.031 30.710 380.020
msPurity.Rcheck/msPurity-Ex.timings
| name | user | system | elapsed | |
| Getfiles | 0.009 | 0.001 | 0.012 | |
| assessPuritySingle | 19.683 | 0.213 | 19.939 | |
| averageAllFragSpectra-purityA-method | 1.303 | 0.058 | 1.362 | |
| averageInterFragSpectra-purityA-method | 3.020 | 0.036 | 3.080 | |
| averageIntraFragSpectra-purityA-method | 5.154 | 0.032 | 5.215 | |
| averageSpectra-purityD-method | 10.107 | 3.576 | 13.720 | |
| averageSpectraSingle | 4.837 | 1.683 | 6.525 | |
| combineAnnotations | 13.309 | 0.230 | 16.207 | |
| createDatabase | 13.967 | 1.253 | 15.257 | |
| createMSP-purityA-method | 0.899 | 0.121 | 1.021 | |
| create_database | 3.213 | 0.163 | 3.474 | |
| dimsPredictPurity-purityD-method | 68.734 | 4.718 | 74.656 | |
| dimsPredictPuritySingle | 0.091 | 0.003 | 0.094 | |
| filterFragSpectra-purityA-method | 0.242 | 0.003 | 0.245 | |
| filterp-purityD-method | 10.010 | 3.207 | 13.571 | |
| flag_remove | 36.336 | 13.668 | 26.996 | |
| frag4feature-purityA-method | 75.892 | 7.407 | 76.627 | |
| getP-purityD-method | 0.004 | 0.000 | 0.004 | |
| get_additional_mzml_meta | 0.035 | 0.002 | 0.037 | |
| groupPeaks-purityD-method | 13.694 | 3.284 | 16.988 | |
| groupPeaksEx | 11.172 | 3.326 | 14.499 | |
| initialize-purityD-method | 0.005 | 0.001 | 0.005 | |
| iwNormGauss | 0.002 | 0.001 | 0.003 | |
| iwNormQE.5 | 0.002 | 0.001 | 0.003 | |
| iwNormRcosine | 0.002 | 0.001 | 0.002 | |
| pcalc | 0.010 | 0.001 | 0.010 | |
| purityA | 17.586 | 0.255 | 17.827 | |
| purityD-class | 0.005 | 0.001 | 0.006 | |
| purityX | 22.734 | 8.391 | 20.958 | |
| spectralMatching | 5.284 | 3.133 | 10.247 | |
| spectral_matching | 0.000 | 0.001 | 0.001 | |
| subtract-purityD-method | 13.047 | 3.899 | 16.946 | |
| subtractMZ | 0.001 | 0.000 | 0.001 | |