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BioC 3.5: CHECK report for MassSpecWavelet on veracruz2

This page was generated on 2017-08-16 13:27:58 -0400 (Wed, 16 Aug 2017).

Package 757/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassSpecWavelet 1.42.0
Pan Du
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/MassSpecWavelet
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  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MassSpecWavelet
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MassSpecWavelet_1.42.0.tar.gz
StartedAt: 2017-08-16 04:51:54 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:52:33 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 38.8 seconds
RetCode: 0
Status:  OK 
CheckDir: MassSpecWavelet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MassSpecWavelet_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MassSpecWavelet.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MassSpecWavelet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassSpecWavelet’ version ‘1.42.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MassSpecWavelet’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to ‘waveslim’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘waveslim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cwt: no visible global function definition for ‘convolve’
extendNBase: no visible global function definition for ‘nextn’
identifyMajorPeaks: no visible global function definition for
  ‘quantile’
identifyMajorPeaks: no visible global function definition for ‘sd’
identifyMajorPeaks: no visible global function definition for ‘mad’
plotLocalMax: no visible global function definition for
  ‘colorRampPalette’
plotLocalMax: no visible global function definition for ‘plot’
plotLocalMax: no visible global function definition for ‘points’
plotPeak: no visible global function definition for ‘plot’
plotPeak: no visible global function definition for ‘points’
plotPeak: no visible global function definition for ‘abline’
plotRidgeList: no visible global function definition for
  ‘colorRampPalette’
plotRidgeList: no visible global function definition for ‘plot’
plotRidgeList: no visible global function definition for ‘points’
sav.gol: no visible binding for global variable ‘coefficients’
smoothDWT: no visible global function definition for ‘dwt’
smoothDWT: no visible global function definition for ‘modwt’
smoothDWT: no visible global function definition for ‘quantile’
smoothDWT : <anonymous>: no visible global function definition for
  ‘quantile’
smoothDWT: no visible global function definition for ‘idwt’
smoothDWT: no visible global function definition for ‘imodwt’
Undefined global functions or variables:
  abline coefficients colorRampPalette convolve dwt idwt imodwt mad
  modwt nextn plot points quantile sd
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "coefficients", "convolve", "mad", "nextn",
             "quantile", "sd")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: getRidgeValue.Rd:24-26: Dropping empty section \examples
prepare_Rd: sav.gol.Rd:28-29: Dropping empty section \examples
prepare_Rd: smoothDWT.Rd:22-25: Dropping empty section \details
prepare_Rd: smoothDWT.Rd:29: Dropping empty section \references
prepare_Rd: smoothDWT.Rd:32-34: Dropping empty section \examples
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MassSpecWavelet.Rcheck/00check.log’
for details.


MassSpecWavelet.Rcheck/00install.out:

* installing *source* package ‘MassSpecWavelet’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c convolve2.c -o convolve2.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MassSpecWavelet.so convolve2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/MassSpecWavelet.Rcheck/MassSpecWavelet/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MassSpecWavelet)

MassSpecWavelet.Rcheck/MassSpecWavelet-Ex.timings:

nameusersystemelapsed
MassSpecWavelet.package2.2300.2572.571
cwt0.4110.0330.458
extendLength0.0010.0000.001
extendNBase0.0010.0000.001
getLocalMaximumCWT0.2260.0290.263
getRidge0.2860.0230.315
identifyMajorPeaks2.8170.1893.084
localMaximum0.0520.0010.054
peakDetectionCWT3.4310.4794.017
plotLocalMax0.2130.0230.248
plotPeak1.5810.2271.867
plotRidgeList0.3110.0230.349
tuneInPeakInfo2.2630.2532.592