BioC 2.14: CHECK report for biovizBase on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.12.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/biovizBase.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.12.3’
* 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 ‘biovizBase’ can be installed ... [26s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.cytobandColor’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
transformToLinkInCircle: no visible binding for global variable
  ‘.circle.x’
transformToLinkInCircle: no visible binding for global variable
  ‘.circle.y’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘from.x’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘from.y’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘to.x’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘to.y’
validEven: no visible binding for global variable ‘gr’
* 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 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 line endings 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 ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
crunch-method 8.852  0.329    9.19
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/biovizBase.Rcheck/00check.log’
for details.

* installing *source* package ‘biovizBase’ ...
** 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 R_init_biovizBase.c -o R_init_biovizBase.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 bin_offsets.c -o bin_offsets.o
bin_offsets.c:57:15: warning: passing 'Rbyte *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
  if (strncmp(b, "BAI\1", 4))
              ^
/usr/include/string.h:84:26: note: passing argument to parameter here
int      strncmp(const char *, const char *, size_t);
                             ^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/biovizBase.Rcheck/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biovizBase)

name	user	system	elapsed
CRC	0.007	0.001	0.007
GCcontent	2.528	0.192	2.725
addStepping-method	1.178	0.058	1.237
aes-utils	0.001	0.000	0.000
colorBlindSafePal	0.001	0.000	0.001
containLetters	0.001	0.000	0.001
crc1.GeRL	0.013	0.000	0.013
crunch-method	8.852	0.329	9.190
darned_hg19_subset500	0.090	0.002	0.091
flatGrl	0.427	0.008	0.436
genesymbol	0.177	0.006	0.184
getBioColor	0.001	0.000	0.002
getFormalNames	0.001	0.000	0.001
getGaps	1.993	0.012	2.006
getIdeoGR	0.555	0.011	0.566
getIdeogram	0	0	0
hg19Ideogram	0.129	0.002	0.131
hg19IdeogramCyto	0.054	0.001	0.055
ideo	0.459	0.002	0.462
ideoCyto	0.529	0.002	0.533
isIdeogram	0.008	0.000	0.009
isMatchedWithModel	0.579	0.031	0.611
isSimpleIdeogram	0.111	0.001	0.111
maxGap-method	0.723	0.010	0.733
pileupAsGRanges	0.000	0.000	0.001
pileupGRangesAsVariantTable	0.001	0.000	0.001
plotColorLegend	0.003	0.000	0.004
scale	0.446	0.007	0.454
showColor	0	0	0
shrinkageFun-method	0.491	0.008	0.499
splitByFacets-method	1.108	0.011	1.119
strip_formula_dots	0.002	0.000	0.002
subsetArgsByFormals	0.001	0.000	0.001
transform	3.336	0.128	3.468
transformGRangesForEvenSpace	0.398	0.009	0.406

BioC 2.14: CHECK report for biovizBase on morelia

Summary

Command output