BioC 2.13: CHECK report for biovizBase on perceval

Package: biovizBase

Version: 1.10.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.10.8.tar.gz

StartedAt: 2014-04-04 23:50:59 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:56:33 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 334.0 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/biovizBase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.10.8’
* 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 ... [30s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fetch: no visible global function definition for
  ‘readBamGappedAlignments’
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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘intro.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
crunch-method 8.339  0.585   8.935
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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/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-2.13-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	3.624	0.426	4.063
addStepping-method	1.449	0.102	1.551
aes-utils	0.002	0.006	0.008
colorBlindSafePal	0.003	0.009	0.012
containLetters	0.002	0.004	0.005
crc1.GeRL	0.017	0.005	0.022
crunch-method	8.339	0.585	8.935
darned_hg19_subset500	0.074	0.005	0.079
flatGrl	0.477	0.020	0.496
genesymbol	0.173	0.017	0.190
getBioColor	0.004	0.006	0.010
getFormalNames	0.002	0.002	0.005
getGaps	2.006	0.030	2.037
getIdeoGR	0.583	0.022	0.605
getIdeogram	0.002	0.003	0.004
hg19Ideogram	0.123	0.004	0.128
hg19IdeogramCyto	0.091	0.011	0.102
isIdeogram	0.007	0.005	0.011
isMatchedWithModel	0.531	0.035	0.566
isSimpleIdeogram	0.082	0.005	0.086
maxGap-method	0.699	0.020	0.719
pileupAsGRanges	0.003	0.005	0.008
pileupGRangesAsVariantTable	0.003	0.005	0.008
plotColorLegend	0.005	0.003	0.008
scale	0.507	0.027	0.534
showColor	0.002	0.003	0.004
shrinkageFun-method	0.511	0.023	0.534
splitByFacets-method	1.329	0.027	1.359
strip_formula_dots	0.003	0.004	0.007
subsetArgsByFormals	0.003	0.005	0.008
transform	3.823	0.200	4.031
transformGRangesForEvenSpace	0.556	0.020	0.582