BioC 3.1: CHECK report for biovizBase on petty

Package: biovizBase

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biovizBase_1.16.0.tar.gz

StartedAt: 2015-10-08 21:43:45 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:49:20 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 335.3 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biovizBase_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.16.0’
* 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 ... [31s/32s] 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’
mold,SummarizedExperiment : .local: no visible global function
  definition for ‘assays’
mold,SummarizedExperiment : .local: no visible global function
  definition for ‘colData’
mold,SummarizedExperiment : .local: no visible global function
  definition for ‘rowRanges’
* 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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
crunch-method 6.774  0.298   7.386
* 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-3.1-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-3.1-bioc/meat/biovizBase.Rcheck/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (biovizBase)

name	user	system	elapsed
CRC	0.007	0.000	0.008
GCcontent	1.697	0.034	1.733
addStepping-method	1.110	0.028	1.139
aes-utils	0.001	0.000	0.001
colorBlindSafePal	0.002	0.001	0.002
containLetters	0.002	0.000	0.002
crc1.GeRL	0.019	0.001	0.020
crunch-method	6.774	0.298	7.386
darned_hg19_subset500	0.064	0.001	0.065
flatGrl	0.582	0.006	0.587
genesymbol	0.170	0.014	0.184
getBioColor	0.002	0.000	0.002
getFormalNames	0.002	0.000	0.001
getGaps	1.857	0.006	1.864
getIdeoGR	0.654	0.008	0.662
getIdeogram	0	0	0
hg19Ideogram	0.043	0.001	0.043
hg19IdeogramCyto	0.043	0.001	0.043
ideo	0.168	0.003	0.170
ideoCyto	0.166	0.002	0.168
isIdeogram	0.004	0.000	0.005
isMatchedWithModel	0.734	0.019	0.752
isSimpleIdeogram	0.033	0.001	0.035
maxGap-method	0.774	0.006	0.780
pileupAsGRanges	0.002	0.001	0.002
pileupGRangesAsVariantTable	0.001	0.000	0.002
plotColorLegend	0.005	0.000	0.005
scale	0.569	0.006	0.574
showColor	0	0	0
shrinkageFun-method	0.624	0.005	0.629
splitByFacets-method	1.586	0.033	1.621
strip_formula_dots	0.002	0.000	0.002
subsetArgsByFormals	0.001	0.001	0.001
transform	3.546	0.209	3.758
transformGRangesForEvenSpace	0.650	0.010	0.661