BioC 3.2: CHECK report for biovizBase on perceval

Package: biovizBase

Version: 1.17.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biovizBase_1.17.1.tar.gz

StartedAt: 2015-08-23 22:38:02 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:43:04 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 301.6 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_1.17.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/biovizBase.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.17.1’
* 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 ... [29s/29s] 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,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’
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’
* 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 ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
crunch-method 5.155  0.262    5.43
* 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_biovizBase.c -o R_init_biovizBase.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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	0.980	0.021	1.019
addStepping-method	0.845	0.007	0.853
aes-utils	0.001	0.000	0.000
colorBlindSafePal	0.001	0.000	0.001
containLetters	0.001	0.000	0.002
crc1.GeRL	0.013	0.001	0.014
crunch-method	5.155	0.262	5.430
darned_hg19_subset500	0.066	0.002	0.068
flatGrl	0.500	0.006	0.506
genesymbol	0.131	0.011	0.142
getBioColor	0.002	0.000	0.002
getFormalNames	0.001	0.000	0.001
getGaps	2.279	0.008	2.288
getIdeoGR	0.534	0.008	0.543
getIdeogram	0.001	0.000	0.000
hg19Ideogram	0.034	0.004	0.039
hg19IdeogramCyto	0.037	0.010	0.049
ideo	0.120	0.035	0.156
ideoCyto	0.135	0.005	0.141
isIdeogram	0.004	0.000	0.005
isMatchedWithModel	0.846	0.025	0.871
isSimpleIdeogram	0.031	0.001	0.033
maxGap-method	0.613	0.008	0.622
pileupAsGRanges	0.001	0.000	0.001
pileupGRangesAsVariantTable	0.001	0.000	0.001
plotColorLegend	0.003	0.000	0.003
scale	0.460	0.005	0.465
showColor	0.001	0.000	0.000
shrinkageFun-method	0.486	0.005	0.491
splitByFacets-method	0.815	0.007	0.824
strip_formula_dots	0.002	0.001	0.002
subsetArgsByFormals	0.001	0.000	0.001
transform	2.667	0.169	2.840
transformGRangesForEvenSpace	0.54	0.01	0.55