Thomas N. Lawson
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/msPurity |
| git_branch: RELEASE_3_16 |
| git_last_commit: f0aecfe |
| git_last_commit_date: 2022-11-01 11:13:46 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:42 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 1281/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| msPurity 1.24.0 (landing page) Thomas N. Lawson
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: msPurity |
| Version: 1.24.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:msPurity.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings msPurity_1.24.0.tar.gz |
| StartedAt: 2023-04-11 03:42:55 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 03:57:18 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 863.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: msPurity.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:msPurity.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings msPurity_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/msPurity.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.24.0'
* 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 19.5Mb
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
* 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
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.
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createDatabase 105.83 1.53 187.11
frag4feature-purityA-method 86.42 0.50 166.11
dimsPredictPurity-purityD-method 31.14 0.67 31.81
combineAnnotations 10.20 0.50 10.74
spectralMatching 5.26 3.47 18.28
flag_remove 8.47 0.21 30.80
assessPuritySingle 7.73 0.15 8.03
groupPeaks-purityD-method 6.80 0.45 7.25
purityA 7.00 0.14 7.14
subtract-purityD-method 6.50 0.28 6.78
groupPeaksEx 5.28 0.45 5.74
purityX 5.02 0.19 23.06
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/msPurity.Rcheck/00check.log'
for details.
msPurity.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL msPurity ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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] "F:/biocbuild/bbs-3.16-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds"
[1] "F:/biocbuild/bbs-3.16-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xset.rds"
[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
177.43 18.45 240.50
msPurity.Rcheck/msPurity-Ex.timings
| name | user | system | elapsed | |
| Getfiles | 0 | 0 | 0 | |
| assessPuritySingle | 7.73 | 0.15 | 8.03 | |
| averageAllFragSpectra-purityA-method | 0.16 | 0.00 | 0.15 | |
| averageInterFragSpectra-purityA-method | 0.40 | 0.01 | 0.42 | |
| averageIntraFragSpectra-purityA-method | 0.44 | 0.00 | 0.44 | |
| averageSpectra-purityD-method | 3.56 | 0.47 | 4.06 | |
| averageSpectraSingle | 1.63 | 0.22 | 1.84 | |
| combineAnnotations | 10.20 | 0.50 | 10.74 | |
| createDatabase | 105.83 | 1.53 | 187.11 | |
| createMSP-purityA-method | 0.15 | 0.02 | 0.16 | |
| create_database | 1.22 | 0.06 | 1.37 | |
| dimsPredictPurity-purityD-method | 31.14 | 0.67 | 31.81 | |
| dimsPredictPuritySingle | 0.02 | 0.02 | 0.03 | |
| filterFragSpectra-purityA-method | 0.06 | 0.00 | 0.07 | |
| filterp-purityD-method | 3.48 | 0.34 | 3.84 | |
| flag_remove | 8.47 | 0.21 | 30.80 | |
| frag4feature-purityA-method | 86.42 | 0.50 | 166.11 | |
| getP-purityD-method | 0 | 0 | 0 | |
| get_additional_mzml_meta | 0.03 | 0.00 | 0.03 | |
| groupPeaks-purityD-method | 6.80 | 0.45 | 7.25 | |
| groupPeaksEx | 5.28 | 0.45 | 5.74 | |
| initialize-purityD-method | 0 | 0 | 0 | |
| iwNormGauss | 0 | 0 | 0 | |
| iwNormQE.5 | 0 | 0 | 0 | |
| iwNormRcosine | 0 | 0 | 0 | |
| pcalc | 0 | 0 | 0 | |
| purityA | 7.00 | 0.14 | 7.14 | |
| purityD-class | 0 | 0 | 0 | |
| purityX | 5.02 | 0.19 | 23.06 | |
| spectralMatching | 5.26 | 3.47 | 18.28 | |
| spectral_matching | 0.02 | 0.00 | 0.02 | |
| subtract-purityD-method | 6.50 | 0.28 | 6.78 | |
| subtractMZ | 0 | 0 | 0 | |