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CHECK report for HilbertVis on celaya2

This page was generated on 2019-10-16 12:47:17 -0400 (Wed, 16 Oct 2019).

Package 759/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HilbertVis 1.42.0
Simon Anders
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/HilbertVis
Branch: RELEASE_3_9
Last Commit: 8c9b51f
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HilbertVis
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HilbertVis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HilbertVis_1.42.0.tar.gz
StartedAt: 2019-10-16 03:38:55 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:39:39 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 43.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: HilbertVis.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HilbertVis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HilbertVis_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/HilbertVis.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HilbertVis/DESCRIPTION’ ... OK
* this is package ‘HilbertVis’ 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 ‘HilbertVis’ can be installed ... WARNING
Found the following significant warnings:
  shrink_vector.c:76:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  shrink_vector.c:76:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/HilbertVis.Rcheck/00install.out’ for details.
* 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 ‘EBImage’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeRandomTestData: no visible global function definition for ‘runif’
makeRandomTestData: no visible global function definition for ‘rgamma’
makeRandomTestData: no visible global function definition for ‘dnorm’
makeRandomTestData: no visible global function definition for ‘rpois’
plotLongVector: no visible global function definition for ‘plot’
plotLongVector: no visible global function definition for ‘segments’
showHilbertImage: no visible global function definition for
  ‘colorRampPalette’
showHilbertImage: no visible global function definition for ‘col2rgb’
showHilbertImage: no visible global function definition for ‘flip’
showHilbertImage: no visible global function definition for ‘rgbImage’
showHilbertImage: no visible global function definition for ‘Image’
showHilbertImage: no visible global function definition for ‘display’
shrinkRleVector: no visible global function definition for ‘aggregate’
shrinkVector: no visible global function definition for ‘is’
Undefined global functions or variables:
  Image aggregate col2rgb colorRampPalette display dnorm flip is plot
  rgamma rgbImage rpois runif segments
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette")
  importFrom("graphics", "plot", "segments")
  importFrom("methods", "is")
  importFrom("stats", "aggregate", "dnorm", "rgamma", "rpois", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘HilbertVisGUI’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/HilbertVis.Rcheck/00check.log’
for details.



Installation output

HilbertVis.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HilbertVis
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘HilbertVis’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c hilbert.c -o hilbert.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c make_wiggle_vector.c -o make_wiggle_vector.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c shrink_vector.c -o shrink_vector.o
shrink_vector.c:76:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
               if( abs( REAL( vector )[ j ] ) > abs( val ) )
                   ^
shrink_vector.c:76:20: note: use function 'fabs' instead
               if( abs( REAL( vector )[ j ] ) > abs( val ) )
                   ^~~
                   fabs
shrink_vector.c:76:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
               if( abs( REAL( vector )[ j ] ) > abs( val ) )
                                                ^
shrink_vector.c:76:49: note: use function 'fabs' instead
               if( abs( REAL( vector )[ j ] ) > abs( val ) )
                                                ^~~
                                                fabs
2 warnings generated.
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 HilbertVis.so hilbert.o make_wiggle_vector.o shrink_vector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-HilbertVis/00new/HilbertVis/libs
** R
** 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 (HilbertVis)

Tests output


Example timings

HilbertVis.Rcheck/HilbertVis-Ex.timings

nameusersystemelapsed
hilbertCurve0.0170.0100.027
hilbertImage3.4280.4524.225
makeRandomTestData000
makeWiggleVector0.0150.0010.017
plotHilbertCurve0.2750.0250.309
plotLongVector0.1250.0160.141
showHilbertImage000
shrinkVector0.0000.0000.001