BioC 3.2: CHECK report for biovizBase on linux1.bioconductor.org

Package: biovizBase

Version: 1.18.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.18.0.tar.gz

StartedAt: 2015-10-27 01:28:38 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:32:02 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 203.5 seconds

RetCode: 0

Status:  OK

CheckDir: biovizBase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/biovizBase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.18.0’
* 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 ... [22s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘BSgenome’ ‘rtracklayer’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genSymbols: no visible binding for global variable ‘start_location’
genSymbols: no visible binding for global variable ‘end_location’
genSymbols: no visible binding for global variable ‘Chromosome’
genSymbols: no visible binding for global variable ‘symbol’
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’
mold,ExpressionSet : .local: no visible global function definition for
  ‘exprs’
mold,ExpressionSet : .local: no visible global function definition for
  ‘pData’
mold,RleList : .local: no visible binding for global variable
  ‘xRleList’
mold,eSet : .local: no visible global function definition for
  ‘phenoData’
mold,eSet : .local: no visible global function definition for ‘melt’
mold,eSet : .local: no visible global function definition for
  ‘varLabels’
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
crunch-method 13.693  0.132  13.826
* 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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/biovizBase.Rcheck/00check.log’
for details.

* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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-3.2-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]
   if (strncmp(b, "BAI\1", 4))
   ^
In file included from /home/biocbuild/bbs-3.2-bioc/R/include/R_ext/RS.h:26:0,
                 from /home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:26,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:399:15: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
 extern size_t strlen (const char *__s)
               ^
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
   ^
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]
In file included from /home/biocbuild/bbs-3.2-bioc/R/include/R_ext/RS.h:26:0,
                 from /home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:26,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:147:12: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
 extern int strncmp (const char *__s1, const char *__s2, size_t __n)
            ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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
CRC	0.005	0.000	0.005
GCcontent	0.398	0.012	0.410
addStepping-method	0.507	0.000	0.508
aes-utils	0.001	0.000	0.000
colorBlindSafePal	0.001	0.000	0.000
containLetters	0.001	0.000	0.001
crc1.GeRL	0.010	0.000	0.009
crunch-method	13.693	0.132	13.826
darned_hg19_subset500	0.050	0.004	0.054
flatGrl	0.198	0.016	0.214
genesymbol	0.093	0.008	0.101
getBioColor	0.001	0.000	0.001
getFormalNames	0	0	0
getGaps	1.036	0.000	1.036
getIdeoGR	0.173	0.004	0.177
getIdeogram	0	0	0
hg19Ideogram	0.018	0.000	0.019
hg19IdeogramCyto	0.022	0.000	0.022
ideo	0.072	0.000	0.072
ideoCyto	0.104	0.000	0.104
isIdeogram	0.004	0.000	0.004
isMatchedWithModel	0.431	0.004	0.435
isSimpleIdeogram	0.028	0.000	0.029
maxGap-method	0.384	0.004	0.389
pileupAsGRanges	0.001	0.000	0.001
pileupGRangesAsVariantTable	0.001	0.000	0.001
plotColorLegend	0.003	0.000	0.003
scale	0.291	0.012	0.303
showColor	0.000	0.000	0.001
shrinkageFun-method	0.297	0.000	0.297
splitByFacets-method	0.675	0.004	0.680
strip_formula_dots	0.002	0.000	0.001
subsetArgsByFormals	0.001	0.000	0.001
transform	1.850	0.044	1.893
transformGRangesForEvenSpace	0.137	0.012	0.149