Thomas N. Lawson
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/msPurity |
| git_branch: RELEASE_3_14 |
| git_last_commit: 82cfdcb |
| git_last_commit_date: 2021-10-26 12:28:01 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:57 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the msPurity package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msPurity.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1225/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| msPurity 1.20.0 (landing page) Thomas N. Lawson
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: msPurity |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:msPurity.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings msPurity_1.20.0.tar.gz |
| StartedAt: 2022-04-12 23:20:59 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 23:53:21 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1941.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: msPurity.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:msPurity.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings msPurity_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/msPurity.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'msPurity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msPurity' version '1.20.0'
* 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 whether package 'msPurity' can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.9Mb
sub-directories of 1Mb or more:
extdata 18.8Mb
* 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
* 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 ... WARNING
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'
createDatabase: no visible global function definition for
'featureValues'
create_database : getxcmsSetObject: no visible global function
definition for 'sampclass<-'
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'
flag_remove: no visible global function definition for
'PeakDensityParam'
flag_remove: no visible global function definition for 'chromPeaks<-'
flag_remove: no visible global function definition for 'chromPeaks'
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'
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'
sum_calc_peaklist: no visible global function definition for
'phenoData'
averageSpectra,purityD: no visible binding for global variable 'i'
subtract,purityD: no visible binding for global variable 'i'
Undefined global functions or variables:
PeakDensityParam accession alli chromPeaks chromPeaks<-
compoundDbname count.fields featureValues grpid i idx inPurity
instrument instrument_type l_speakmetaFiltered
library_spectra_meta_id lower match_factor mtch mtchi name.y parallel
pass_flag phenoData 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createDatabase 119.01 2.45 215.27
frag4feature-purityA-method 102.51 0.23 187.30
dimsPredictPurity-purityD-method 33.61 1.11 34.71
spectralMatching 10.92 1.67 85.10
combineAnnotations 11.50 0.39 12.20
assessPuritySingle 10.52 0.06 11.66
flag_remove 9.94 0.28 50.68
purityA 8.31 0.04 8.35
groupPeaks-purityD-method 7.04 0.94 7.97
purityX 6.17 0.18 25.80
groupPeaksEx 4.59 1.16 5.75
subtract-purityD-method 4.45 1.00 5.46
filterp-purityD-method 4.35 1.02 5.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createDatabase 128.10 0.84 213.81
frag4feature-purityA-method 117.53 0.13 216.62
dimsPredictPurity-purityD-method 31.14 0.72 31.86
combineAnnotations 12.14 0.40 12.53
assessPuritySingle 9.75 0.08 9.83
spectralMatching 7.94 1.84 9.94
flag_remove 9.42 0.18 34.92
purityA 9.23 0.06 9.28
groupPeaks-purityD-method 6.11 0.97 7.07
purityX 6.25 0.21 25.20
groupPeaksEx 5.07 1.22 6.30
subtract-purityD-method 4.53 0.75 5.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/msPurity.Rcheck/00check.log'
for details.
msPurity.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/msPurity_1.20.0.tar.gz && rm -rf msPurity.buildbin-libdir && mkdir msPurity.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=msPurity.buildbin-libdir msPurity_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL msPurity_1.20.0.zip && rm msPurity_1.20.0.tar.gz msPurity_1.20.0.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 11.2M 0 51086 0 0 321k 0 0:00:35 --:--:-- 0:00:35 321k
14 11.2M 14 1703k 0 0 1474k 0 0:00:07 0:00:01 0:00:06 1474k
37 11.2M 37 4283k 0 0 1990k 0 0:00:05 0:00:02 0:00:03 1990k
67 11.2M 67 7774k 0 0 2468k 0 0:00:04 0:00:03 0:00:01 2467k
100 11.2M 100 11.2M 0 0 2881k 0 0:00:04 0:00:04 --:--:-- 2882k
install for i386
* installing *source* package 'msPurity' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'msPurity'
finding HTML links ... done
Getfiles html
assessPuritySingle html
averageAllFragSpectra-purityA-method html
averageInterFragSpectra-purityA-method
html
averageIntraFragSpectra-purityA-method
html
averageSpectra-purityD-method html
averageSpectraSingle html
combineAnnotations html
createDatabase html
createMSP-purityA-method html
create_database html
dimsPredictPurity-purityD-method html
dimsPredictPuritySingle html
filterFragSpectra-purityA-method html
filterp-purityD-method html
flag_remove html
frag4feature-purityA-method html
getP-purityD-method html
get_additional_mzml_meta html
groupPeaks-purityD-method html
groupPeaksEx html
initialize-purityD-method html
iwNormGauss html
iwNormQE.5 html
iwNormRcosine html
msPurity html
pcalc html
purityA html
purityD-class html
purityX html
show-purityA-method html
show-purityD-method html
show-purityX-method html
spectralMatching html
spectral_matching html
subtract-purityD-method html
subtractMZ html
validate-purityA-method html
writeOut-purityD-method html
** 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
install for x64
* installing *source* package 'msPurity' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msPurity' as msPurity_1.20.0.zip
* DONE (msPurity)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'msPurity' successfully unpacked and MD5 sums checked
|
msPurity.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> 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 (fillpeaks) ##"
[1] "########################################################"
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds"
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xset.rds"
Warning message:
In FUN(...) :
(corrected) retention time vector length mismatch for LCMSMS_1.mzML
Warning message:
In FUN(...) :
(corrected) retention time vector length mismatch for LCMSMS_2.mzML
[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 frag4feature (xcms v2 functions) ##"
[1] "########################################################"
[1] "\n"
[1] "####################################################################"
[1] "## Checking frag4feature (fillpeaks) (xcms v2 functions) ##"
[1] "####################################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking filterFragSpectra (xcms v2 functions) ##"
[1] "########################################################"
[1] "\n"
[1] "##############################################################"
[1] "## Checking averageIntraFragSpectra (xcms v2 functions) ##"
[1] "##############################################################"
[1] "\n"
[1] "#############################################################"
[1] "## Checking averageInterFragSpectra (xcms v2 functions) #"
[1] "#############################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageAllFragSpectra (xcms v2 functions) #"
[1] "########################################################"
[1] "\n"
[1] "###########################################################################"
[1] "## Checking averageIntraFragSpectra (with filter) (xcms v2 functions) ##"
[1] "###########################################################################"
[1] "\n"
[1] "############################################################################"
[1] "## Checking averageInterFragSpectra (with filter) (xcms v2 functions) ##"
[1] "############################################################################"
[1] "\n"
[1] "#########################################################################"
[1] "## Checking averageAllFragSpectra (with filter) (xcms v2 functions) ##"
[1] "#########################################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking createMSP functions (xcms v2 functions) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## checking flag and remove (lc-ms) ##"
[1] "########################################################"
[1] "\n"
[1] "#######################################################"
[1] "## Checking database (new schema) ##"
[1] "#######################################################"
[1] "\n"
[1] "###############################################################"
[1] "## Checking database (new schema) (xcms v2 functions) ##"
[1] "###############################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking database (old 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] "## Testing spectral matching (spectralMatching) q(scan) v q ##"
[1] "#################################################################"
[1] "\n"
[1] "############################################################################"
[1] "## Testing spectral matching (spectralMatching) qvl (xcms v2 functions) ##"
[1] "############################################################################"
[1] "\n"
[1] "############################################################################"
[1] "## Testing spectral matching (spectralMatching) qvq (xcms v2 functions) ##"
[1] "############################################################################"
[1] "\n"
[1] "######################################################################################"
[1] "## Testing spectral matching (spectralMatching) q(scan) v q (xcms v2 functions) ##"
[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"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 306 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
226.87 20.18 294.78
|
msPurity.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> 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 (fillpeaks) ##"
[1] "########################################################"
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds"
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xset.rds"
Warning message:
In FUN(...) :
(corrected) retention time vector length mismatch for LCMSMS_2.mzML
Warning message:
In FUN(...) :
(corrected) retention time vector length mismatch for LCMSMS_1.mzML
[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 frag4feature (xcms v2 functions) ##"
[1] "########################################################"
[1] "\n"
[1] "####################################################################"
[1] "## Checking frag4feature (fillpeaks) (xcms v2 functions) ##"
[1] "####################################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking filterFragSpectra (xcms v2 functions) ##"
[1] "########################################################"
[1] "\n"
[1] "##############################################################"
[1] "## Checking averageIntraFragSpectra (xcms v2 functions) ##"
[1] "##############################################################"
[1] "\n"
[1] "#############################################################"
[1] "## Checking averageInterFragSpectra (xcms v2 functions) #"
[1] "#############################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageAllFragSpectra (xcms v2 functions) #"
[1] "########################################################"
[1] "\n"
[1] "###########################################################################"
[1] "## Checking averageIntraFragSpectra (with filter) (xcms v2 functions) ##"
[1] "###########################################################################"
[1] "\n"
[1] "############################################################################"
[1] "## Checking averageInterFragSpectra (with filter) (xcms v2 functions) ##"
[1] "############################################################################"
[1] "\n"
[1] "#########################################################################"
[1] "## Checking averageAllFragSpectra (with filter) (xcms v2 functions) ##"
[1] "#########################################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking createMSP functions (xcms v2 functions) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## checking flag and remove (lc-ms) ##"
[1] "########################################################"
[1] "\n"
[1] "#######################################################"
[1] "## Checking database (new schema) ##"
[1] "#######################################################"
[1] "\n"
[1] "###############################################################"
[1] "## Checking database (new schema) (xcms v2 functions) ##"
[1] "###############################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking database (old 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] "## Testing spectral matching (spectralMatching) q(scan) v q ##"
[1] "#################################################################"
[1] "\n"
[1] "############################################################################"
[1] "## Testing spectral matching (spectralMatching) qvl (xcms v2 functions) ##"
[1] "############################################################################"
[1] "\n"
[1] "############################################################################"
[1] "## Testing spectral matching (spectralMatching) qvq (xcms v2 functions) ##"
[1] "############################################################################"
[1] "\n"
[1] "######################################################################################"
[1] "## Testing spectral matching (spectralMatching) q(scan) v q (xcms v2 functions) ##"
[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"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 306 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
218.76 15.00 285.29
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msPurity.Rcheck/examples_i386/msPurity-Ex.timings
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msPurity.Rcheck/examples_x64/msPurity-Ex.timings
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