BioC 3.1: CHECK report for adSplit on zin2

Package: adSplit

Version: 1.38.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings adSplit_1.38.0.tar.gz

StartedAt: 2015-10-08 22:18:41 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:21:40 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 178.8 seconds

RetCode: 0

Status:  OK

CheckDir: adSplit.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings adSplit_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/adSplit.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 ‘adSplit/DESCRIPTION’ ... OK
* this is package ‘adSplit’ version ‘1.38.0’
* 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 ... [7s/7s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [109s/115s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
randomDiana2means 35.844  0.220  36.112
makeEID2PROBESenv 33.437  0.208  34.083
drawRandomPS      32.372  0.191  37.940
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/adSplit.Rcheck/00check.log’
for details.

* installing *source* package ‘adSplit’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-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]
     throw Tomato(__LINE__, "tscore: internal error, shame on the programmer");
                                                                             ^
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]
       throw Tomato(__LINE__, "isis() called with unknown function");
                                                                   ^
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o adSplit.so adSplit.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/adSplit.Rcheck/adSplit/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (adSplit)

name	user	system	elapsed
adSplit	2.478	0.104	2.583
diana2means	1.129	0.008	1.139
drawRandomPS	32.372	0.191	37.940
golubKEGGSplits	0.001	0.000	0.002
hist.splitSet	0.007	0.000	0.006
image.splitSet	0.122	0.004	0.137
makeEID2PROBESenv	33.437	0.208	34.083
print.splitSet	0.002	0.000	0.003
randomDiana2means	35.844	0.220	36.112