BioC 3.2: CHECK report for biovizBase on oaxaca

Package: biovizBase

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biovizBase_1.18.0.tar.gz

StartedAt: 2016-04-22 22:11:53 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:16:46 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 293.0 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.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 biovizBase_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/biovizBase.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.18.0’
* 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 ‘biovizBase’ can be installed ... [27s/28s] 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘BSgenome’ ‘rtracklayer’
  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
genSymbols: no visible binding for global variable ‘start_location’
genSymbols: no visible binding for global variable ‘end_location’
genSymbols: no visible binding for global variable ‘Chromosome’
genSymbols: no visible binding for global variable ‘symbol’
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’
mold,ExpressionSet : .local: no visible global function definition for
  ‘exprs’
mold,ExpressionSet : .local: no visible global function definition for
  ‘pData’
mold,RleList : .local: no visible binding for global variable
  ‘xRleList’
mold,eSet : .local: no visible global function definition for
  ‘phenoData’
mold,eSet : .local: no visible global function definition for ‘melt’
mold,eSet : .local: no visible global function definition for
  ‘varLabels’
* 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 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 ... [39s/40s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
crunch-method 15.994  0.661  16.757
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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/Library/Frameworks/R.framework/Resources/lib -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-3.2-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	0.008
GCcontent	0.735	0.011	0.764
addStepping-method	0.766	0.006	0.775
aes-utils	0.000	0.000	0.001
colorBlindSafePal	0.001	0.000	0.002
containLetters	0.001	0.000	0.002
crc1.GeRL	0.016	0.001	0.017
crunch-method	15.994	0.661	16.757
darned_hg19_subset500	0.048	0.007	0.055
flatGrl	0.343	0.032	0.375
genesymbol	0.147	0.010	0.157
getBioColor	0.002	0.000	0.002
getFormalNames	0.000	0.001	0.001
getGaps	1.586	0.036	1.630
getIdeoGR	0.342	0.005	0.348
getIdeogram	0.001	0.000	0.001
hg19Ideogram	0.030	0.001	0.031
hg19IdeogramCyto	0.037	0.001	0.038
ideo	0.131	0.002	0.132
ideoCyto	0.123	0.002	0.126
isIdeogram	0.004	0.001	0.005
isMatchedWithModel	0.525	0.014	0.539
isSimpleIdeogram	0.022	0.001	0.023
maxGap-method	0.372	0.005	0.378
pileupAsGRanges	0.001	0.000	0.001
pileupGRangesAsVariantTable	0.001	0.000	0.001
plotColorLegend	0.002	0.001	0.003
scale	0.348	0.006	0.355
showColor	0.000	0.000	0.001
shrinkageFun-method	0.308	0.005	0.313
splitByFacets-method	0.653	0.006	0.660
strip_formula_dots	0.002	0.001	0.002
subsetArgsByFormals	0.001	0.000	0.001
transform	2.358	0.121	2.480
transformGRangesForEvenSpace	0.271	0.004	0.274