Thomas N. Lawson
| Snapshot Date: 2020-04-13 16:45:33 -0400 (Mon, 13 Apr 2020) |
| URL: https://git.bioconductor.org/packages/msPurity |
| Branch: RELEASE_3_10 |
| Last Commit: 2c0f0f1 |
| Last Changed Date: 2020-03-26 13:49:40 -0400 (Thu, 26 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-14 13:21:23 -0400 (Tue, 14 Apr 2020).
| Package 1103/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| msPurity 1.12.2 Thomas N. Lawson
| malbec1 | Linux (Ubuntu 18.04.4 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: msPurity |
| Version: 1.12.2 |
| 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_1.12.2.tar.gz |
| StartedAt: 2020-04-14 04:12:15 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 04:22:50 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 634.2 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_1.12.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/msPurity.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.2’
* 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
addGenericMS1LookupResults: no visible global function definition for
‘count.fields’
addMetFragResults: no visible global function definition for
‘count.fields’
addSiriusResults: no visible global function definition for
‘count.fields’
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 count.fields 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
Consider adding
importFrom("utils", "count.fields")
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 64.079 3.663 64.044
dimsPredictPurity-purityD-method 56.716 2.268 59.864
flag_remove 27.343 6.686 19.440
purityX 16.663 4.139 14.315
combineAnnotations 16.514 0.390 17.060
assessPuritySingle 16.335 0.102 16.582
purityA 14.054 0.143 14.318
spectralMatching 9.345 2.808 13.318
createDatabase 10.660 0.614 11.390
subtract-purityD-method 8.007 1.793 9.885
groupPeaks-purityD-method 7.947 1.823 9.841
groupPeaksEx 6.842 1.598 8.501
filterp-purityD-method 5.701 1.627 7.453
averageSpectra-purityD-method 5.038 1.955 7.066
* 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-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 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: 176 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
258.615 18.685 262.085
msPurity.Rcheck/msPurity-Ex.timings
| name | user | system | elapsed | |
| Getfiles | 0.009 | 0.000 | 0.010 | |
| assessPuritySingle | 16.335 | 0.102 | 16.582 | |
| averageAllFragSpectra-purityA-method | 1.043 | 0.021 | 1.076 | |
| averageInterFragSpectra-purityA-method | 2.405 | 0.013 | 2.442 | |
| averageIntraFragSpectra-purityA-method | 3.982 | 0.014 | 4.029 | |
| averageSpectra-purityD-method | 5.038 | 1.955 | 7.066 | |
| averageSpectraSingle | 2.412 | 0.906 | 3.340 | |
| combineAnnotations | 16.514 | 0.390 | 17.060 | |
| createDatabase | 10.660 | 0.614 | 11.390 | |
| createMSP-purityA-method | 0.592 | 0.041 | 0.635 | |
| create_database | 2.211 | 0.070 | 2.304 | |
| dimsPredictPurity-purityD-method | 56.716 | 2.268 | 59.864 | |
| dimsPredictPuritySingle | 0.060 | 0.001 | 0.061 | |
| filterFragSpectra-purityA-method | 0.193 | 0.001 | 0.196 | |
| filterp-purityD-method | 5.701 | 1.627 | 7.453 | |
| flag_remove | 27.343 | 6.686 | 19.440 | |
| frag4feature-purityA-method | 64.079 | 3.663 | 64.044 | |
| getP-purityD-method | 0.004 | 0.000 | 0.004 | |
| get_additional_mzml_meta | 0.037 | 0.001 | 0.039 | |
| groupPeaks-purityD-method | 7.947 | 1.823 | 9.841 | |
| groupPeaksEx | 6.842 | 1.598 | 8.501 | |
| initialize-purityD-method | 0.003 | 0.000 | 0.003 | |
| iwNormGauss | 0.001 | 0.000 | 0.002 | |
| iwNormQE.5 | 0.001 | 0.000 | 0.001 | |
| iwNormRcosine | 0.001 | 0.000 | 0.001 | |
| pcalc | 0.008 | 0.002 | 0.009 | |
| purityA | 14.054 | 0.143 | 14.318 | |
| purityD-class | 0.004 | 0.000 | 0.004 | |
| purityX | 16.663 | 4.139 | 14.315 | |
| spectralMatching | 9.345 | 2.808 | 13.318 | |
| spectral_matching | 0.001 | 0.000 | 0.000 | |
| subtract-purityD-method | 8.007 | 1.793 | 9.885 | |
| subtractMZ | 0.001 | 0.000 | 0.001 | |