BioC 3.0: CHECK report for adSplit on zin1

Package: adSplit

Version: 1.36.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings adSplit_1.36.0.tar.gz

StartedAt: 2015-04-09 21:19:14 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:23:12 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 237.9 seconds

RetCode: 0

Status:  OK

CheckDir: adSplit.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings adSplit_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/adSplit.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adSplit/DESCRIPTION’ ... OK
* this is package ‘adSplit’ version ‘1.36.0’
* 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 ‘adSplit’ can be installed ... [9s/10s] 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 loading without being on the library search path ... 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 ... OK
* 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 GNU extensions in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [137s/144s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
randomDiana2means 44.999  0.272  45.511
makeEID2PROBESenv 41.606  0.212  43.289
drawRandomPS      39.995  0.284  45.107
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/adSplit.Rcheck/00check.log’
for details.

* installing *source* package ‘adSplit’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c adSplit.cpp -o adSplit.o
adSplit.cpp: In function ‘double tscore(double*, int, int, split&, isis_pars&)’:
adSplit.cpp:256:77: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
adSplit.cpp: In function ‘void isis(char**, double*, int*, int*, int*, int*, int*, double*, int*)’:
adSplit.cpp:469:67: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o adSplit.so adSplit.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/adSplit.Rcheck/adSplit/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 (adSplit)

name	user	system	elapsed
adSplit	2.956	0.080	3.314
diana2means	1.316	0.032	1.350
drawRandomPS	39.995	0.284	45.107
golubKEGGSplits	0.004	0.000	0.002
hist.splitSet	0.008	0.000	0.008
image.splitSet	0.280	0.008	0.414
makeEID2PROBESenv	41.606	0.212	43.289
print.splitSet	0.004	0.000	0.003
randomDiana2means	44.999	0.272	45.511