Thomas N. Lawson
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/msPurity |
| Branch: master |
| Last Commit: 166e189 |
| Last Changed Date: 2019-01-17 06:52:30 -0400 (Thu, 17 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:16:19 -0400 (Tue, 09 Apr 2019).
| Package 1039/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| msPurity 1.9.8 Thomas N. Lawson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: msPurity |
| Version: 1.9.8 |
| 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_1.9.8.tar.gz |
| StartedAt: 2019-04-09 03:48:55 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:19:01 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 1806.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: msPurity.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.9.8.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/msPurity.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.8’
* 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 ... OK
* 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
CV: no visible global function definition for ‘sd’
Getfiles: no visible global function definition for ‘fix’
assessPuritySingle: no visible binding for global variable ‘parallel’
averageCluster: no visible global function definition for ‘sd’
averageCluster: no visible global function definition for ‘median’
averageSpectraSingle: no visible binding for global variable ‘scanid’
average_spectra: no visible global function definition for ‘median’
covar: no visible global function definition for ‘sd’
dimsPredictPuritySingle: no visible global function definition for
‘read.csv’
dimsPredictPuritySingleMz: no visible global function definition for
‘png’
dimsPredictPuritySingleMz: no visible binding for global variable
‘mtchi’
dimsPredictPuritySingleMz: no visible binding for global variable
‘alli’
dimsPredictPuritySingleMz: no visible global function definition for
‘points’
dimsPredictPuritySingleMz: no visible binding for global variable
‘mtch’
dimsPredictPuritySingleMz: no visible global function definition for
‘text’
dimsPredictPuritySingleMz: no visible global function definition for
‘dev.off’
dimsPredictPuritySingleMz: no visible global function definition for
‘median’
dimsPredictPuritySingleMz: no visible global function definition for
‘sd’
export_2_sqlite: no visible global function definition for ‘read.table’
export_2_sqlite: no visible global function definition for ‘read.csv’
flag_remove: no visible global function definition for ‘write.csv’
get_topn: no visible binding for global variable ‘topn’
groupPeaksEx: no visible binding for global variable ‘median’
iwNormGauss: no visible global function definition for ‘dnorm’
iwNormGauss: no visible global function definition for ‘approxfun’
iwNormQE.5: no visible global function definition for ‘approxfun’
iwNormRcosine: no visible global function definition for ‘approxfun’
linearPurity: no visible global function definition for ‘approxfun’
medGroup: no visible binding for global variable ‘median’
median_match_results: no visible global function definition for
‘median’
msfrProcess: no visible global function definition for ‘read.csv’
performHc: no visible global function definition for ‘dist’
performHc: no visible global function definition for ‘as.dist’
plotPurity: no visible global function definition for ‘png’
plotPurity: no visible binding for global variable ‘idx’
plotPurity: no visible binding for global variable ‘purity’
plotPurity: no visible binding for global variable ‘variable’
plotPurity: no visible global function definition for ‘dev.off’
plotPurity: no visible global function definition for ‘write.csv’
pp4file: no visible global function definition for ‘png’
pp4file: no visible global function definition for ‘plot’
pp4file: no visible global function definition for ‘lines’
pp4file: no visible global function definition for ‘legend’
pp4file: no visible global function definition for ‘abline’
pp4file: no visible global function definition for ‘dev.off’
pp4file: no visible global function definition for ‘median’
predictPurityLCMSloop: no visible global function definition for
‘median’
predictPurityLCMSloop : <anonymous>: no visible global function
definition for ‘na.omit’
predictPurityLCMSloop : <anonymous>: no visible global function
definition for ‘median’
predictPurityLCMSloop : <anonymous>: no visible global function
definition for ‘sd’
purityA: no visible binding for global variable ‘i’
removeIsotopes: no visible global function definition for ‘write.csv’
rsd: no visible global function definition for ‘sd’
rsde: no visible global function definition for ‘sd’
snrFilter: no visible global function definition for ‘median’
stde: no visible global function definition for ‘sd’
stderror: no visible global function definition for ‘sd’
sum_calc_peaklist: no visible binding for global variable ‘median’
write_msp_single: no visible global function definition for
‘packageVersion’
xcmsGroupPurity: no visible binding for global variable ‘median’
xcmsGroupPurity: no visible global function definition for ‘median’
averageSpectra,purityD: no visible binding for global variable ‘i’
subtract,purityD: no visible binding for global variable ‘i’
validate,purityA: no visible global function definition for ‘head’
writeOut,purityD: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
abline alli approxfun as.dist dev.off dist dnorm fix head i idx
legend lines median mtch mtchi na.omit packageVersion parallel plot
png points purity read.csv read.table scanid sd text topn variable
write.csv
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "abline", "legend", "lines", "plot", "points",
"text")
importFrom("stats", "approxfun", "as.dist", "dist", "dnorm", "median",
"na.omit", "sd")
importFrom("utils", "fix", "head", "packageVersion", "read.csv",
"read.table", "write.csv")
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
spectral_matching 202.594 13.072 217.123
averageAllFragSpectra-purityA-method 92.374 2.306 94.987
frag4feature-purityA-method 81.877 1.236 89.250
averageInterFragSpectra-purityA-method 80.344 1.236 82.392
create_database 78.628 1.168 80.107
createMSP-purityA-method 75.810 1.519 77.454
averageIntraFragSpectra-purityA-method 76.077 1.085 77.174
dimsPredictPurity-purityD-method 63.882 3.809 68.172
flag_remove 29.275 2.836 32.273
purityX 19.381 2.494 21.842
assessPuritySingle 17.942 0.185 18.116
purityA 17.716 0.166 17.903
groupPeaks-purityD-method 13.754 3.346 17.103
subtract-purityD-method 13.746 3.032 16.779
groupPeaksEx 12.186 3.256 15.450
averageSpectra-purityD-method 12.128 2.927 15.058
filterp-purityD-method 9.579 3.393 13.595
averageSpectraSingle 5.716 1.591 7.308
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-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 in method for ‘averageIntraFragSpectra’ with signature ‘"purityA"’: no definition for class “purityA” in method for ‘averageInterFragSpectra’ with signature ‘"purityA"’: no definition for class “purityA” in method for ‘averageAllFragSpectra’ with signature ‘"purityA"’: no definition for class “purityA” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (msPurity)
msPurity.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(msPurity)
Loading required package: Rcpp
> Sys.setenv("R_TESTS" = "")
> test_check("msPurity")
[1] "########################################################"
[1] "## Checking LCMS based class and functions ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Checking LCMS based class and functions ##"
[1] "########################################################"
[1] 6
[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"
[1] "########################################################"
[1] "## checking flag and remove (lc-ms) ##"
[1] "########################################################"
class
LCMS_1 blank
LCMS_2 blank
LCMSMS_1 sample
LCMSMS_2 sample
mzmed mzmin mzmax rtmed rtmin rtmax npeaks blank sample
1 144.0287 144.0284 144.0290 47.37034 46.92627 47.81441 2 0 2
2 166.0550 166.0549 166.0551 64.89254 64.60541 65.17967 2 0 2
3 180.9095 180.9089 180.9102 41.02660 40.95480 41.09841 2 0 2
4 188.1108 188.1108 188.1108 60.70048 60.63481 60.76616 2 0 2
5 219.0095 219.0092 219.0097 41.75565 41.68466 41.82664 2 0 2
6 260.9744 260.9731 260.9757 38.72353 38.65304 38.79402 2 0 2
LCMS_1 LCMS_2 LCMSMS_1 LCMSMS_2 blank_median_I sample_median_I blank_RSD_I
1 NA NA 2484505 2537180 NA 2510843 NA
2 NA NA 56932287 55568583 NA 56250435 NA
3 NA NA 18476700 17988709 NA 18232705 NA
4 NA NA 14925267 13776153 NA 14350710 NA
5 NA NA 38065038 37309939 NA 37687488 NA
6 NA NA 17290367 17220189 NA 17255278 NA
sample_RSD_I blank_coverage sample_coverage blank_RSD_RT sample_RSD_RT
1 1.4834625 0 1 NA 1.3257418
2 1.7142699 0 1 NA 0.6257405
3 1.8925417 0 1 NA 0.2475310
4 5.6620664 0 1 NA 0.1530134
5 1.4167453 0 1 NA 0.2404352
6 0.2875833 0 1 NA 0.2574441
rsd_all_RT grpid blank_valid sample_valid all_sample_valid mzmin_full
1 1.3257418 1 0 1 1 143.9969
2 0.6257405 2 0 1 1 166.0530
3 0.2475310 3 0 1 1 180.8942
4 0.1530134 4 0 1 1 188.1105
5 0.2404352 5 0 1 1 218.9426
6 0.2574441 6 0 1 1 260.9275
mzmax_full rtmin_full rtmax_full
1 144.0323 34.04152 59.86578
2 166.0862 52.21429 77.26732
3 181.0492 28.20627 52.98104
4 188.1110 46.16103 74.29742
5 219.0265 29.08403 53.73766
6 261.0371 25.57753 50.69718
[1] "########################################################"
[1] "## Checking LCMS based class and functions ##"
[1] "########################################################"
[1] 4
[1] "########################################################"
[1] "## Checking pcalc functions ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Spectral matching functions ##"
[1] "########################################################"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 105 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
708.772 71.343 750.337
msPurity.Rcheck/msPurity-Ex.timings
| name | user | system | elapsed | |
| Getfiles | 0.005 | 0.000 | 0.006 | |
| assessPuritySingle | 17.942 | 0.185 | 18.116 | |
| averageAllFragSpectra-purityA-method | 92.374 | 2.306 | 94.987 | |
| averageInterFragSpectra-purityA-method | 80.344 | 1.236 | 82.392 | |
| averageIntraFragSpectra-purityA-method | 76.077 | 1.085 | 77.174 | |
| averageSpectra-purityD-method | 12.128 | 2.927 | 15.058 | |
| averageSpectraSingle | 5.716 | 1.591 | 7.308 | |
| createMSP-purityA-method | 75.810 | 1.519 | 77.454 | |
| create_database | 78.628 | 1.168 | 80.107 | |
| dimsPredictPurity-purityD-method | 63.882 | 3.809 | 68.172 | |
| dimsPredictPuritySingle | 0.092 | 0.003 | 0.107 | |
| filterp-purityD-method | 9.579 | 3.393 | 13.595 | |
| flag_remove | 29.275 | 2.836 | 32.273 | |
| frag4feature-purityA-method | 81.877 | 1.236 | 89.250 | |
| getP-purityD-method | 0.005 | 0.000 | 0.006 | |
| get_additional_mzml_meta | 0.034 | 0.002 | 0.035 | |
| groupPeaks-purityD-method | 13.754 | 3.346 | 17.103 | |
| groupPeaksEx | 12.186 | 3.256 | 15.450 | |
| initialize-purityD-method | 0.004 | 0.000 | 0.003 | |
| iwNormGauss | 0.002 | 0.000 | 0.003 | |
| iwNormQE.5 | 0.002 | 0.000 | 0.002 | |
| iwNormRcosine | 0.001 | 0.000 | 0.002 | |
| pcalc | 0.007 | 0.000 | 0.007 | |
| purityA | 17.716 | 0.166 | 17.903 | |
| purityD-class | 0.005 | 0.001 | 0.006 | |
| purityX | 19.381 | 2.494 | 21.842 | |
| spectral_matching | 202.594 | 13.072 | 217.123 | |
| subtract-purityD-method | 13.746 | 3.032 | 16.779 | |
| subtractMZ | 0.000 | 0.000 | 0.001 | |