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CHECK report for adSplit on malbec1

This page was generated on 2018-04-12 13:07:36 -0400 (Thu, 12 Apr 2018).

Package 14/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adSplit 1.48.0
Claudio Lottaz
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/adSplit
Branch: RELEASE_3_6
Last Commit: 57dfcd9
Last Changed Date: 2017-10-30 12:39:16 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: adSplit
Version: 1.48.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings adSplit_1.48.0.tar.gz
StartedAt: 2018-04-11 21:19:13 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:22:36 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 203.1 seconds
RetCode: 0
Status:  OK 
CheckDir: adSplit.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings adSplit_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/adSplit.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.48.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeEID2PROBESenv 39.256  0.176  39.929
randomDiana2means 36.216  0.180  36.434
drawRandomPS      32.432  0.116  32.581
* 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-3.6-bioc/meat/adSplit.Rcheck/00check.log’
for details.



Installation output

adSplit.Rcheck/00install.out

* installing *source* package ‘adSplit’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -L/usr/local/lib -o adSplit.so adSplit.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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)

Tests output


Example timings

adSplit.Rcheck/adSplit-Ex.timings

nameusersystemelapsed
adSplit3.1600.1123.511
diana2means1.6640.0442.274
drawRandomPS32.432 0.11632.581
golubKEGGSplits0.0000.0000.001
hist.splitSet0.0040.0000.006
image.splitSet0.1440.0200.170
makeEID2PROBESenv39.256 0.17639.929
print.splitSet0.0000.0000.002
randomDiana2means36.216 0.18036.434