BioC 3.4: CHECK report for seqTools on morelia

Package: seqTools

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqTools_1.8.0.tar.gz

StartedAt: 2017-04-15 08:00:23 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:00:50 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 27.6 seconds

RetCode: 0

Status:  OK

CheckDir: seqTools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqTools_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/seqTools.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 ‘seqTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqTools’ version ‘1.8.0’
* 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 ‘seqTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sim_fq: no visible global function definition for ‘hclust’
sim_fq: no visible global function definition for ‘as.dist’
plotGCcontent,Fastqq: no visible global function definition for ‘plot’
plotGCcontent,Fastqq: no visible global function definition for ‘lines’
plotGCcontent,Fastqq: no visible global function definition for
  ‘legend’
plotKmerCount,Fastqq: no visible global function definition for ‘plot’
plotKmerCount,Fastqq: no visible global function definition for ‘lines’
plotKmerCount,Fastqq: no visible global function definition for ‘axis’
plotKmerCount,Fastqq: no visible global function definition for
  ‘legend’
plotMergedPhredQuant,Fastqq: no visible global function definition for
  ‘plot’
plotMergedPhredQuant,Fastqq: no visible global function definition for
  ‘lines’
plotMergedPhredQuant,Fastqq: no visible global function definition for
  ‘legend’
plotNucCount,Fastqq: no visible global function definition for ‘plot’
plotNucCount,Fastqq: no visible global function definition for ‘lines’
plotNucCount,Fastqq: no visible global function definition for ‘legend’
plotNucFreq,Fastqq: no visible global function definition for ‘plot’
plotNucFreq,Fastqq: no visible global function definition for ‘lines’
plotNucFreq,Fastqq: no visible global function definition for ‘legend’
plotPhredDist,Fastqq: no visible global function definition for
  ‘topo.colors’
plotPhredDist,Fastqq: no visible global function definition for ‘plot’
plotPhredDist,Fastqq: no visible global function definition for ‘axis’
plotPhredQuant,Fastqq: no visible global function definition for ‘plot’
plotPhredQuant,Fastqq: no visible global function definition for
  ‘lines’
plotPhredQuant,Fastqq: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis hclust legend lines plot topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/seqTools.Rcheck/00check.log’
for details.

* installing *source* package ‘seqTools’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c seqTools.c -o seqTools.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 seqTools.so seqTools.o -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/seqTools.Rcheck/seqTools/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 (seqTools)

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