BioC 3.4: CHECK report for biovizBase on morelia

Package: biovizBase

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biovizBase_1.22.0.tar.gz

StartedAt: 2017-04-14 23:16:37 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:21:46 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 308.6 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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.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 ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.22.0’
* 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 ... 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: no visible global function definition for 'exprs'
mold,ExpressionSet: no visible global function definition for 'pData'
mold,RleList: no visible binding for global variable 'xRleList'
mold,eSet: no visible global function definition for 'phenoData'
mold,eSet: no visible global function definition for 'melt'
mold,eSet: no visible global function definition for 'varLabels'
Undefined global functions or variables:
  .circle.x .circle.y Chromosome end_location exprs from.x from.y melt
  pData phenoData start_location symbol to.x to.y varLabels xRleList
* 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 ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
crunch-method 18.338   0.74  21.087
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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-3.4-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	0.547	0.028	0.615
addStepping-method	0.612	0.014	0.626
aes-utils	0.000	0.000	0.001
colorBlindSafePal	0.001	0.000	0.001
containLetters	0.001	0.000	0.001
crc1.GeRL	0.011	0.000	0.011
crunch-method	18.338	0.740	21.087
darned_hg19_subset500	0.041	0.001	0.043
flatGrl	0.253	0.005	0.257
genesymbol	0.137	0.010	0.147
getBioColor	0.001	0.000	0.002
getFormalNames	0.000	0.000	0.001
getGaps	1.160	0.006	1.167
getIdeoGR	0.243	0.005	0.248
getIdeogram	0.000	0.001	0.000
hg19Ideogram	0.016	0.001	0.018
hg19IdeogramCyto	0.021	0.001	0.022
ideo	0.057	0.002	0.058
ideoCyto	0.072	0.002	0.074
isIdeogram	0.004	0.001	0.004
isMatchedWithModel	0.390	0.015	0.404
isSimpleIdeogram	0.033	0.001	0.033
maxGap-method	0.352	0.005	0.357
pileupAsGRanges	0	0	0
pileupGRangesAsVariantTable	0.001	0.000	0.001
plotColorLegend	0.003	0.000	0.004
scale	0.220	0.004	0.225
showColor	0.001	0.000	0.000
shrinkageFun-method	0.228	0.004	0.231
splitByFacets-method	0.487	0.005	0.492
strip_formula_dots	0.001	0.000	0.001
subsetArgsByFormals	0.001	0.000	0.001
transform	2.700	0.108	2.812
transformGRangesForEvenSpace	0.229	0.003	0.233