BioC 2.13: CHECK report for biovizBase on zin1

Package: biovizBase

Version: 1.10.8

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.10.8.tar.gz

StartedAt: 2014-04-04 23:54:51 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:58:08 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 196.9 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/biovizBase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [18s/18s] 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 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 ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
crunch-method 6.429  0.128   6.608
* 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/biovizBase.Rcheck/00check.log’
for details.

* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
/usr/include/string.h:399:15: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign]
/usr/include/string.h:146:12: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
gcc -std=gnu99 -shared -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/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	2.492	0.136	2.639
addStepping-method	1.032	0.032	1.076
aes-utils	0.000	0.004	0.002
colorBlindSafePal	0.000	0.004	0.004
containLetters	0.004	0.000	0.003
crc1.GeRL	0.012	0.004	0.015
crunch-method	6.429	0.128	6.608
darned_hg19_subset500	0.060	0.000	0.057
flatGrl	0.304	0.016	0.320
genesymbol	0.164	0.000	0.166
getBioColor	0.000	0.000	0.003
getFormalNames	0.000	0.004	0.002
getGaps	1.540	0.008	1.555
getIdeoGR	0.404	0.004	0.409
getIdeogram	0	0	0
hg19Ideogram	0.092	0.000	0.091
hg19IdeogramCyto	0.056	0.000	0.056
isIdeogram	0.004	0.000	0.004
isMatchedWithModel	0.300	0.016	0.316
isSimpleIdeogram	0.068	0.000	0.070
maxGap-method	0.464	0.012	0.476
pileupAsGRanges	0.000	0.000	0.001
pileupGRangesAsVariantTable	0.004	0.000	0.002
plotColorLegend	0.004	0.000	0.005
scale	0.352	0.008	0.359
showColor	0.000	0.000	0.001
shrinkageFun-method	0.340	0.012	0.354
splitByFacets-method	0.860	0.012	0.874
strip_formula_dots	0.000	0.000	0.002
subsetArgsByFormals	0.004	0.000	0.001
transform	2.672	0.048	2.724
transformGRangesForEvenSpace	0.272	0.012	0.283