Thomas N. Lawson
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/msPurity |
| Branch: RELEASE_3_11 |
| Last Commit: b5e27ab |
| Last Changed Date: 2020-10-06 11:59:27 -0400 (Tue, 06 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:13 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE msPurity PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1143/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| msPurity 1.14.1 Thomas N. Lawson
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: msPurity |
| Version: 1.14.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:msPurity.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings msPurity_1.14.1.tar.gz |
| StartedAt: 2020-10-17 06:17:43 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:41:12 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1409.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: msPurity.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:msPurity.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings msPurity_1.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/msPurity.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.14.1'
* 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 12.7Mb
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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dimsPredictPurity-purityD-method 49.36 1.15 50.53
frag4feature-purityA-method 47.51 0.30 65.19
combineAnnotations 16.33 0.55 17.11
createDatabase 14.20 1.41 16.42
purityA 14.31 0.13 15.18
assessPuritySingle 11.39 0.08 11.95
spectralMatching 8.55 2.53 228.06
flag_remove 10.19 0.42 48.46
purityX 8.75 0.84 35.00
groupPeaks-purityD-method 7.86 1.26 9.12
groupPeaksEx 6.41 1.25 7.66
subtract-purityD-method 5.69 1.39 7.08
filterp-purityD-method 5.12 1.02 6.14
averageSpectra-purityD-method 4.56 1.06 5.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
frag4feature-purityA-method 37.53 0.17 54.98
dimsPredictPurity-purityD-method 36.62 0.97 37.63
combineAnnotations 11.46 0.44 11.89
createDatabase 10.69 0.34 11.03
assessPuritySingle 10.87 0.05 10.92
purityA 8.47 0.11 8.55
spectralMatching 6.42 1.86 8.28
flag_remove 8.00 0.05 30.67
groupPeaks-purityD-method 6.36 1.00 7.36
purityX 6.61 0.22 25.62
filterp-purityD-method 5.47 1.23 6.72
subtract-purityD-method 5.63 0.75 6.38
groupPeaksEx 5.09 1.06 6.16
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/msPurity.Rcheck/00check.log'
for details.
msPurity.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/msPurity_1.14.1.tar.gz && rm -rf msPurity.buildbin-libdir && mkdir msPurity.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=msPurity.buildbin-libdir msPurity_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL msPurity_1.14.1.zip && rm msPurity_1.14.1.tar.gz msPurity_1.14.1.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
100 7457k 100 7457k 0 0 9121k 0 --:--:-- --:--:-- --:--:-- 9172k
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_1.14.1.zip
* DONE (msPurity)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'msPurity' successfully unpacked and MD5 sums checked
|
msPurity.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 ##"
[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] "## Testing spectral matching (spectralMatching) q(scan) v q ##"
[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: 184 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
199.31 17.73 257.59
|
msPurity.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 ##"
[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] "## Testing spectral matching (spectralMatching) q(scan) v q ##"
[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: 184 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
191.34 13.43 247.01
|
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msPurity.Rcheck/examples_i386/msPurity-Ex.timings
|
msPurity.Rcheck/examples_x64/msPurity-Ex.timings
|