Package: MassSpecWavelet

Version: 1.50.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MassSpecWavelet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MassSpecWavelet_1.50.0.tar.gz

StartedAt: 2019-10-16 04:56:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:57:48 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 56.4 seconds

RetCode: 0

Status:  OK

CheckDir: MassSpecWavelet.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MassSpecWavelet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MassSpecWavelet_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MassSpecWavelet.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MassSpecWavelet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MassSpecWavelet' version '1.50.0'
* 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 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
* 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
'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 : : 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/MassSpecWavelet/libs/i386/MassSpecWavelet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/MassSpecWavelet/libs/x64/MassSpecWavelet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/MassSpecWavelet.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MassSpecWavelet_1.50.0.tar.gz && rm -rf MassSpecWavelet.buildbin-libdir && mkdir MassSpecWavelet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MassSpecWavelet.buildbin-libdir MassSpecWavelet_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MassSpecWavelet_1.50.0.zip && rm MassSpecWavelet_1.50.0.tar.gz MassSpecWavelet_1.50.0.zip
###
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install for i386

* installing *source* package 'MassSpecWavelet' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c convolve2.c -o convolve2.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o MassSpecWavelet.dll tmp.def convolve2.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MassSpecWavelet.buildbin-libdir/00LOCK-MassSpecWavelet/00new/MassSpecWavelet/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MassSpecWavelet'
    finding HTML links ... done
    MassSpecWavelet.package                 html  
    cwt                                     html  
    exampleMS                               html  
    extendLength                            html  
    extendNBase                             html  
    getLocalMaximumCWT                      html  
    getRidge                                html  
    getRidgeLength                          html  
    getRidgeValue                           html  
    identifyMajorPeaks                      html  
    localMaximum                            html  
    mzInd2vRange                            html  
    mzV2indRange                            html  
    peakDetectionCWT                        html  
    plotLocalMax                            html  
    plotPeak                                html  
    plotRidgeList                           html  
    sav.gol                                 html  
    smoothDWT                               html  
    tuneInPeakInfo                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MassSpecWavelet' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c convolve2.c -o convolve2.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o MassSpecWavelet.dll tmp.def convolve2.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MassSpecWavelet.buildbin-libdir/MassSpecWavelet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MassSpecWavelet' as MassSpecWavelet_1.50.0.zip
* DONE (MassSpecWavelet)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MassSpecWavelet' successfully unpacked and MD5 sums checked