Package: biovizBase

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.6.2.tar.gz

StartedAt: 2013-03-24 22:45:20 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:49:28 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 248.2 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/biovizBase.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'biovizBase/DESCRIPTION' ... OK
* this is package 'biovizBase' version '1.6.2'
* 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 whether package 'biovizBase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/biovizBase.Rcheck/00check.log'
for details.

* installing *source* package 'biovizBase' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -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
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.11-bioc/meat/biovizBase.Rcheck/biovizBase/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'intro.Rnw' 
** testing if installed package can be loaded

* DONE (biovizBase)

name	user	system	elapsed
GCcontent	2.829	0.488	3.395
addStepping-method	1.430	0.090	1.534
aes-utils	0.001	0.001	0.000
colorBlindSafePal	0	0	0
containLetters	0	0	0
crc1.GeRL	0.014	0.002	0.016
darned_hg19_subset500	0.050	0.002	0.052
flatGrl	0.304	0.024	0.333
genesymbol	0.182	0.013	0.198
getBioColor	0.001	0.000	0.002
getFormalNames	0	0	0
getGaps	1.646	0.021	1.674
getIdeoGR	0.494	0.027	0.528
getIdeogram	0.000	0.000	0.001
hg19Ideogram	0.097	0.001	0.098
hg19IdeogramCyto	0.034	0.001	0.036
isIdeogram	0.004	0.002	0.017
isMatchedWithModel	0.373	0.036	0.414
isSimpleIdeogram	0.071	0.002	0.076
maxGap-method	0.877	0.016	0.895
pileupAsGRanges	0.000	0.001	0.000
pileupGRangesAsVariantTable	0	0	0
plotColorLegend	0.003	0.002	0.004
scale	0.374	0.017	0.391
showColor	0	0	0
shrinkageFun-method	0.336	0.019	0.360
splitByFacets-method	0.716	0.019	0.737
strip_formula_dots	0.001	0.000	0.002
subsetArgsByFormals	0	0	0
transform	2.883	0.175	3.106
transformGRangesForEvenSpace	0.320	0.013	0.336