Thomas N. Lawson
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/msPurity |
| Branch: master |
| Last Commit: 029aa5d |
| Last Changed Date: 2019-10-29 13:41:29 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:45:20 -0500 (Thu, 16 Jan 2020).
| Package 1100/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| msPurity 1.13.0 Thomas N. Lawson
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: msPurity |
| Version: 1.13.0 |
| 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_1.13.0.tar.gz |
| StartedAt: 2020-01-16 06:46:09 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 06:59:50 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 820.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: msPurity.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/msPurity.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 ‘msPurity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msPurity’ version ‘1.13.0’
* 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 12.4Mb
sub-directories of 1Mb or more:
extdata 11.8Mb
* 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
Namespaces in Imports field not imported from:
‘dbplyr’ ‘jsonlite’ ‘uuid’
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
assessPuritySingle: no visible binding for global variable ‘parallel’
combineAnnotations: no visible binding for global variable
‘compoundDbname’
dimsPredictPuritySingleMz: no visible binding for global variable
‘mtchi’
dimsPredictPuritySingleMz: no visible binding for global variable
‘alli’
dimsPredictPuritySingleMz: no visible binding for global variable
‘mtch’
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’
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’
get_topn: no visible binding for global variable ‘topn’
getxcmsSetObject: no visible global function definition for
‘sampclass<-’
matchi: no visible global function definition for ‘match_factor’
plotPurity: no visible binding for global variable ‘idx’
plotPurity: no visible binding for global variable ‘purity’
plotPurity: no visible binding for global variable ‘variable’
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’
averageSpectra,purityD: no visible binding for global variable ‘i’
subtract,purityD: no visible binding for global variable ‘i’
Undefined global functions or variables:
accession alli compoundDbname grpid i idx inPurity instrument
instrument_type l_speakmetaFiltered library_spectra_meta_id lower
match_factor mtch mtchi name.y parallel pass_flag pid polarity
precursor_mz purity ra retention_time sampclass<- spectraType
spectrum_type topn type variable
* 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 (user + system) or elapsed time > 5s
user system elapsed
frag4feature-purityA-method 84.754 9.611 85.517
dimsPredictPurity-purityD-method 71.310 3.984 75.697
flag_remove 39.306 17.125 30.359
purityX 25.730 12.183 24.739
assessPuritySingle 19.943 0.209 20.145
createDatabase 17.300 1.611 18.927
purityA 18.305 0.235 18.541
combineAnnotations 18.104 0.297 18.418
groupPeaks-purityD-method 13.300 3.500 16.801
spectralMatching 9.874 5.498 17.121
subtract-purityD-method 11.849 3.272 15.121
groupPeaksEx 11.656 2.759 14.417
filterp-purityD-method 11.130 2.698 14.318
averageSpectra-purityD-method 9.081 2.781 11.868
averageSpectraSingle 4.456 1.235 5.692
averageIntraFragSpectra-purityA-method 5.121 0.019 5.140
* 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-3.11-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/4.0/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 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.
> 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: 169 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
290.992 37.006 302.608
msPurity.Rcheck/msPurity-Ex.timings
| name | user | system | elapsed | |
| Getfiles | 0.011 | 0.001 | 0.014 | |
| assessPuritySingle | 19.943 | 0.209 | 20.145 | |
| averageAllFragSpectra-purityA-method | 1.699 | 0.071 | 1.771 | |
| averageInterFragSpectra-purityA-method | 2.865 | 0.042 | 2.908 | |
| averageIntraFragSpectra-purityA-method | 5.121 | 0.019 | 5.140 | |
| averageSpectra-purityD-method | 9.081 | 2.781 | 11.868 | |
| averageSpectraSingle | 4.456 | 1.235 | 5.692 | |
| combineAnnotations | 18.104 | 0.297 | 18.418 | |
| createDatabase | 17.300 | 1.611 | 18.927 | |
| createMSP-purityA-method | 0.980 | 0.178 | 1.157 | |
| create_database | 2.438 | 0.093 | 2.581 | |
| dimsPredictPurity-purityD-method | 71.310 | 3.984 | 75.697 | |
| dimsPredictPuritySingle | 0.078 | 0.002 | 0.081 | |
| filterFragSpectra-purityA-method | 0.290 | 0.001 | 0.292 | |
| filterp-purityD-method | 11.130 | 2.698 | 14.318 | |
| flag_remove | 39.306 | 17.125 | 30.359 | |
| frag4feature-purityA-method | 84.754 | 9.611 | 85.517 | |
| getP-purityD-method | 0.004 | 0.000 | 0.005 | |
| get_additional_mzml_meta | 0.034 | 0.002 | 0.036 | |
| groupPeaks-purityD-method | 13.300 | 3.500 | 16.801 | |
| groupPeaksEx | 11.656 | 2.759 | 14.417 | |
| initialize-purityD-method | 0.006 | 0.000 | 0.007 | |
| iwNormGauss | 0.001 | 0.000 | 0.002 | |
| iwNormQE.5 | 0.002 | 0.000 | 0.002 | |
| iwNormRcosine | 0.002 | 0.000 | 0.003 | |
| pcalc | 0.009 | 0.000 | 0.010 | |
| purityA | 18.305 | 0.235 | 18.541 | |
| purityD-class | 0.005 | 0.001 | 0.005 | |
| purityX | 25.730 | 12.183 | 24.739 | |
| spectralMatching | 9.874 | 5.498 | 17.121 | |
| spectral_matching | 0.001 | 0.000 | 0.001 | |
| subtract-purityD-method | 11.849 | 3.272 | 15.121 | |
| subtractMZ | 0.000 | 0.001 | 0.001 | |