Thomas N. Lawson
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/msPurity |
| Branch: RELEASE_3_7 |
| Last Commit: a9e6c12 |
| Last Changed Date: 2018-06-10 09:48:41 -0400 (Sun, 10 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:42:21 -0400 (Wed, 17 Oct 2018).
| Package 956/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| msPurity 1.6.2 Thomas N. Lawson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: msPurity |
| Version: 1.6.2 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:msPurity.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings msPurity_1.6.2.tar.gz |
| StartedAt: 2018-10-17 03:31:57 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:56:13 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 1456.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: msPurity.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:msPurity.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings msPurity_1.6.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/msPurity.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.2'
* 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 ... OK
* checking for portable file names ... 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
* 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
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'
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'
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'
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'
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 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", "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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
spectral_matching 86.78 2.99 380.97
frag4feature-purityA-method 42.41 1.20 44.44
dimsPredictPurity-purityD-method 34.77 1.50 36.26
assessPuritySingle 14.69 0.11 15.22
purityX 12.72 1.09 13.77
subtract-purityD-method 8.56 1.22 9.78
purityA 9.22 0.09 9.29
groupPeaks-purityD-method 6.81 1.28 8.11
groupPeaksEx 4.47 1.22 5.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
spectral_matching 94.99 2.43 97.39
frag4feature-purityA-method 47.88 0.59 48.56
dimsPredictPurity-purityD-method 37.47 1.40 38.89
purityX 13.26 0.59 13.80
subtract-purityD-method 9.45 1.35 10.81
assessPuritySingle 10.32 0.06 10.35
purityA 9.06 0.05 9.08
groupPeaks-purityD-method 6.29 0.96 7.25
groupPeaksEx 4.52 1.42 5.93
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-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/3.7/bioc/src/contrib/msPurity_1.6.2.tar.gz && rm -rf msPurity.buildbin-libdir && mkdir msPurity.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=msPurity.buildbin-libdir msPurity_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL msPurity_1.6.2.zip && rm msPurity_1.6.2.tar.gz msPurity_1.6.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'msPurity' ...
** 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
averageSpectra-purityD-method html
averageSpectraSingle html
create_database html
dimsPredictPurity-purityD-method html
dimsPredictPuritySingle html
filterp-purityD-method 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
pcalc html
purityA html
purityD-class html
purityX html
show-purityA-method html
show-purityD-method html
show-purityX-method 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
In R CMD INSTALL
install for x64
* installing *source* package 'msPurity' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msPurity' as msPurity_1.6.2.zip
* DONE (msPurity)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'msPurity' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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msPurity.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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] "########################################################"
[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 LCMS based class and functions ##"
[1] "########################################################"
[1] 4
[1] "########################################################"
[1] "## Checking pcalc functions ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Spectral matching functions ##"
[1] "########################################################"
== testthat results ===========================================================
OK: 86 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
222.01 3.85 276.84
|
msPurity.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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] "########################################################"
[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 LCMS based class and functions ##"
[1] "########################################################"
[1] 4
[1] "########################################################"
[1] "## Checking pcalc functions ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Spectral matching functions ##"
[1] "########################################################"
== testthat results ===========================================================
OK: 86 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
256.26 3.57 313.93
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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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