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 | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings msPurity_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/msPurity.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 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 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dimsPredictPurity-purityD-method 31.724 2.896 34.667
frag4feature-purityA-method 29.276 0.252 30.200
purityX 12.104 0.296 12.502
subtract-purityD-method 6.896 3.356 10.273
assessPuritySingle 9.520 0.044 9.786
purityA 9.376 0.072 9.454
groupPeaks-purityD-method 5.744 2.816 8.570
groupPeaksEx 3.876 3.048 6.934
averageSpectra-purityD-method 3.376 3.016 6.433
filterp-purityD-method 2.800 2.964 5.777
* 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
‘/home/biocbuild/bbs-3.5-bioc/meat/msPurity.Rcheck/00check.log’
for details.