BioC 2.14: CHECK report for biovizBase on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.12.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/biovizBase.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ... [21s/21s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/30s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
crunch-method 6.709  0.068    6.79
* 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
  ‘/home/biocbuild/bbs-2.14-bioc/meat/biovizBase.Rcheck/00check.log’
for details.

* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
/usr/include/string.h:399:15: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign]
/usr/include/string.h:146:12: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
gcc -std=gnu99 -shared -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/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	0.008	0.000	0.006
GCcontent	2.364	0.108	2.473
addStepping-method	0.940	0.048	0.990
aes-utils	0	0	0
colorBlindSafePal	0.004	0.000	0.000
containLetters	0.000	0.000	0.001
crc1.GeRL	0.012	0.000	0.012
crunch-method	6.709	0.068	6.790
darned_hg19_subset500	0.068	0.000	0.067
flatGrl	0.300	0.004	0.306
genesymbol	0.156	0.000	0.159
getBioColor	0.004	0.000	0.002
getFormalNames	0.000	0.000	0.001
getGaps	1.532	0.016	1.552
getIdeoGR	0.392	0.012	0.402
getIdeogram	0.000	0.000	0.001
hg19Ideogram	0.100	0.000	0.099
hg19IdeogramCyto	0.044	0.004	0.047
ideo	0.376	0.000	0.424
ideoCyto	0.428	0.000	0.444
isIdeogram	0.008	0.000	0.009
isMatchedWithModel	0.42	0.02	0.47
isSimpleIdeogram	0.080	0.004	0.082
maxGap-method	0.472	0.016	0.490
pileupAsGRanges	0	0	0
pileupGRangesAsVariantTable	0.000	0.000	0.001
plotColorLegend	0.004	0.000	0.003
scale	0.316	0.004	0.319
showColor	0	0	0
shrinkageFun-method	0.344	0.012	0.354
splitByFacets-method	0.864	0.008	0.875
strip_formula_dots	0.000	0.000	0.001
subsetArgsByFormals	0.000	0.000	0.001
transform	2.524	0.056	2.584
transformGRangesForEvenSpace	0.28	0.02	0.30

BioC 2.14: CHECK report for biovizBase on zin2

Summary

Command output