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BioC 3.4: CHECK report for HilbertVis on morelia

This page was generated on 2017-04-15 16:22:52 -0400 (Sat, 15 Apr 2017).

Package 593/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HilbertVis 1.32.0
Simon Anders
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/HilbertVis
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HilbertVis
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HilbertVis_1.32.0.tar.gz
StartedAt: 2017-04-15 03:37:07 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 03:37:40 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 32.6 seconds
RetCode: 0
Status:  OK 
CheckDir: HilbertVis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HilbertVis_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/HilbertVis.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HilbertVis/DESCRIPTION’ ... OK
* this is package ‘HilbertVis’ version ‘1.32.0’
* 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 ... 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 ‘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 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-3.4-bioc/meat/HilbertVis.Rcheck/00check.log’
for details.


HilbertVis.Rcheck/00install.out:

* installing *source* package ‘HilbertVis’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hilbert.c -o hilbert.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c make_wiggle_vector.c -o make_wiggle_vector.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c shrink_vector.c -o shrink_vector.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 HilbertVis.so hilbert.o make_wiggle_vector.o shrink_vector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/HilbertVis.Rcheck/HilbertVis/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HilbertVis)

HilbertVis.Rcheck/HilbertVis-Ex.timings:

nameusersystemelapsed
hilbertCurve0.0080.0020.011
hilbertImage2.6350.1664.652
makeRandomTestData0.0000.0000.001
makeWiggleVector0.0010.0010.001
plotHilbertCurve0.2230.0130.575
plotLongVector0.0620.0070.224
showHilbertImage0.0010.0000.000
shrinkVector0.0010.0000.001