BioC 3.5: CHECK report for seqTools on oaxaca

Package: seqTools

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqTools_1.9.0.tar.gz

StartedAt: 2017-03-04 09:00:46 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:01:16 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 30.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: seqTools.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqTools_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/seqTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.9.0’
* 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’
  Running ‘test_seqTools.r’
 ERROR
Running the tests in ‘tests/test_seqTools.r’ failed.
Last 13 lines of output:
  > library(seqTools)
  Loading required package: zlibbioc
  > 
  > filename <- "test_seqTools.r"
  > basedir <- system.file("extdata", package = "seqTools")
  > 
  > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
  > ## countDnaKmers
  > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
  > 
  > if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT))
  +     stop("[countDnaKmers] Test 1 '", filename, "' FAILED!")
  Error in identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1),  : 
    object 'cdk_ACGT' not found
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/seqTools.Rcheck/00check.log’
for details.

R Under development (unstable) (2017-02-15 r72177) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> library(seqTools)
Loading required package: zlibbioc
> 
> filename <- "test_seqTools.r"
> basedir <- system.file("extdata", package = "seqTools")
> 
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## countDnaKmers
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> 
> if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT))
+     stop("[countDnaKmers] Test 1 '", filename, "' FAILED!")
Error in identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1),  : 
  object 'cdk_ACGT' not found
Execution halted

* installing *source* package ‘seqTools’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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-3.5-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)

name	user	system	elapsed