msPurity 1.2.0
Thomas N. Lawson
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/msPurity | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf msPurity.buildbin-libdir msPurity.Rcheck && mkdir msPurity.buildbin-libdir msPurity.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msPurity.buildbin-libdir msPurity_1.2.0.tar.gz >msPurity.Rcheck\00install.out 2>&1 && cp msPurity.Rcheck\00install.out msPurity-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=msPurity.buildbin-libdir --install="check:msPurity-install.out" --force-multiarch --no-vignettes --timings msPurity_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/msPurity.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.2.0'
* 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 ... 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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'
get_interp_purity: possible error in splinePurity(rowi, roi_scns,
minoff, maxoff, ppm, mostIntense, scanids, plotP, plotdir, isotopes,
im): unused arguments (isotopes, im)
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'
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'
purityX: no visible binding for global variable 'median'
purityX: no visible global function definition for 'median'
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'
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 scanid sd text 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", "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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dimsPredictPurity-purityD-method 31.34 1.27 33.25
frag4feature-purityA-method 28.38 0.43 29.71
purityX 15.38 0.82 25.22
assessPuritySingle 10.42 0.11 12.51
subtract-purityD-method 8.01 1.36 9.38
purityA 7.86 0.11 7.95
groupPeaks-purityD-method 5.84 1.05 6.89
averageSpectra-purityD-method 4.39 1.57 6.28
groupPeaksEx 4.11 1.09 5.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dimsPredictPurity-purityD-method 43.81 1.39 45.27
frag4feature-purityA-method 34.27 0.36 34.78
purityX 14.25 0.53 14.72
subtract-purityD-method 11.11 1.17 12.28
assessPuritySingle 11.27 0.06 11.38
purityA 10.86 0.05 10.89
groupPeaks-purityD-method 6.89 1.25 8.14
groupPeaksEx 4.44 1.26 5.71
averageSpectra-purityD-method 4.44 1.19 5.63
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/msPurity.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'msPurity' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'msPurity' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msPurity' as msPurity_1.2.0.zip
* DONE (msPurity)