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CHECK report for MassSpecWavelet on malbec1

This page was generated on 2021-05-06 12:28:08 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MassSpecWavelet package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1008/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassSpecWavelet 1.56.0  (landing page)
Pan Du
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MassSpecWavelet
Branch: RELEASE_3_12
Last Commit: 0e274f0
Last Changed Date: 2020-10-27 10:30:55 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MassSpecWavelet
Version: 1.56.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MassSpecWavelet.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MassSpecWavelet_1.56.0.tar.gz
StartedAt: 2021-05-06 03:06:05 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:06:37 -0400 (Thu, 06 May 2021)
EllapsedTime: 31.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MassSpecWavelet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MassSpecWavelet.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MassSpecWavelet_1.56.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MassSpecWavelet.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.56.0’
* 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 ‘points’
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 ‘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 points quantile sd
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "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 ... NOTE
Note: information on .o files is not available
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/MassSpecWavelet.Rcheck/00check.log’
for details.



Installation output

MassSpecWavelet.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MassSpecWavelet
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘MassSpecWavelet’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c convolve2.c -o convolve2.o
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o MassSpecWavelet.so convolve2.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-MassSpecWavelet/00new/MassSpecWavelet/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MassSpecWavelet)

Tests output


Example timings

MassSpecWavelet.Rcheck/MassSpecWavelet-Ex.timings

nameusersystemelapsed
MassSpecWavelet.package1.5240.0561.584
cwt0.4800.0080.489
extendLength000
extendNBase000
getLocalMaximumCWT0.3280.0120.339
getRidge0.3120.0000.313
identifyMajorPeaks2.5880.0122.604
localMaximum0.0480.0040.050
peakDetectionCWT3.3400.0563.398
plotLocalMax0.1400.0040.146
plotPeak1.7520.0081.784
plotRidgeList0.3080.0000.309
tuneInPeakInfo2.2720.0002.279