BioC 2.12: CHECK report for biovizBase on petty

Package: biovizBase

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.8.1.tar.gz

StartedAt: 2013-10-08 21:45:08 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:51:15 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 366.7 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/biovizBase.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'biovizBase/DESCRIPTION' ... OK
* this is package 'biovizBase' version '1.8.1'
* 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 ... [34s/34s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [37s/38s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
transform 4.913  0.229   5.187
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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  -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  -c bin_offsets.c -o bin_offsets.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.12-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
GCcontent	4.051	0.400	4.514
addStepping-method	1.671	0.101	1.778
aes-utils	0.002	0.005	0.007
colorBlindSafePal	0.005	0.010	0.017
containLetters	0.002	0.005	0.007
crc1.GeRL	0.028	0.007	0.034
darned_hg19_subset500	0.079	0.008	0.086
flatGrl	0.482	0.037	0.527
genesymbol	0.253	0.020	0.277
getBioColor	0.006	0.010	0.016
getFormalNames	0.003	0.005	0.007
getGaps	2.590	0.041	2.739
getIdeoGR	0.676	0.025	0.752
getIdeogram	0.002	0.004	0.006
hg19Ideogram	0.145	0.009	0.154
hg19IdeogramCyto	0.056	0.005	0.061
isIdeogram	0.009	0.007	0.015
isMatchedWithModel	0.571	0.045	0.619
isSimpleIdeogram	0.114	0.021	0.136
maxGap-method	0.877	0.020	0.903
pileupAsGRanges	0.003	0.006	0.009
pileupGRangesAsVariantTable	0.004	0.006	0.010
plotColorLegend	0.006	0.004	0.010
scale	0.553	0.032	0.591
showColor	0.003	0.005	0.007
shrinkageFun-method	0.532	0.023	0.556
splitByFacets-method	1.137	0.032	1.175
strip_formula_dots	0.004	0.005	0.009
subsetArgsByFormals	0.003	0.006	0.009
transform	4.913	0.229	5.187
transformGRangesForEvenSpace	0.517	0.019	0.580