Package: biovizBase

Version: 1.7.8

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.7.8.tar.gz

StartedAt: 2013-03-25 00:21:59 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:28:22 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 383.4 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/biovizBase.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.7.8’
* 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 ... [36s/36s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [34s/35s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/biovizBase.Rcheck/00check.log’
for details.

* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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-2.12-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-2.12-bioc/R/lib -lR
installing to /home/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
   ‘intro.Rnw’ 
** testing if installed package can be loaded
* DONE (biovizBase)

name	user	system	elapsed
GCcontent	3.365	0.384	3.777
addStepping-method	1.648	0.056	1.704
aes-utils	0.000	0.004	0.006
colorBlindSafePal	0.008	0.004	0.013
containLetters	0.000	0.004	0.006
crc1.GeRL	0.024	0.008	0.031
darned_hg19_subset500	0.052	0.004	0.057
flatGrl	0.384	0.004	0.408
genesymbol	0.168	0.016	0.187
getBioColor	0.008	0.004	0.010
getFormalNames	0.008	0.000	0.005
getGaps	1.984	0.040	2.045
getIdeoGR	0.528	0.004	0.537
getIdeogram	0.004	0.000	0.004
hg19Ideogram	0.112	0.000	0.113
hg19IdeogramCyto	0.064	0.004	0.067
isIdeogram	0.012	0.000	0.009
isMatchedWithModel	0.408	0.016	0.425
isSimpleIdeogram	0.108	0.000	0.107
maxGap-method	0.708	0.004	0.711
pileupAsGRanges	0.008	0.000	0.008
pileupGRangesAsVariantTable	0.008	0.000	0.008
plotColorLegend	0.008	0.000	0.009
scale	0.456	0.012	0.466
showColor	0.004	0.000	0.005
shrinkageFun-method	0.396	0.016	0.412
splitByFacets-method	0.912	0.020	0.935
strip_formula_dots	0.016	0.000	0.013
subsetArgsByFormals	0.008	0.000	0.006
transform	3.821	0.116	4.161
transformGRangesForEvenSpace	0.432	0.008	0.448