Package: biovizBase

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.4.2.tar.gz

StartedAt: 2012-09-23 23:28:14 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:32:23 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 249.7 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/biovizBase.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.4.2'
* 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 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-2.10-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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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-2.10-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	3.339	0.364	3.733
addStepping-method	1.101	0.034	1.137
aes-utils	0	0	0
colorBlindSafePal	0	0	0
containLetters	0.000	0.000	0.001
crc1.GeRL	0.015	0.001	0.016
darned_hg19_subset500	0.275	0.031	0.307
flatGrl	0.299	0.019	0.318
genesymbol	0.196	0.009	0.205
getBioColor	0.001	0.000	0.001
getFormalNames	0.000	0.000	0.001
getGaps	1.277	0.019	1.295
getIdeoGR	0.491	0.018	0.509
getIdeogram	0	0	0
hg19Ideogram	0.075	0.001	0.077
hg19IdeogramCyto	0.036	0.001	0.037
isIdeogram	0.004	0.002	0.006
isMatchedWithModel	0.368	0.035	0.403
isSimpleIdeogram	0.051	0.001	0.053
maxGap-method	0.520	0.013	0.533
pileupAsGRanges	0	0	0
pileupGRangesAsVariantTable	0	0	0
plotColorLegend	0.003	0.001	0.004
scale	0.284	0.013	0.295
showColor	0	0	0
shrinkageFun-method	0.288	0.012	0.300
splitByFacets-method	0.626	0.015	0.642
strip_formula_dots	0.000	0.000	0.001
subsetArgsByFormals	0.001	0.000	0.001
transform	3.179	0.159	3.338
transformGRangesForEvenSpace	0.281	0.015	0.296