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CHECK report for adSplit on malbec2

This page was generated on 2019-04-09 11:24:39 -0400 (Tue, 09 Apr 2019).

Package 19/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adSplit 1.53.0
Claudio Lottaz
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/adSplit
Branch: master
Last Commit: bbc5ba0
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: adSplit
Version: 1.53.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:adSplit.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings adSplit_1.53.0.tar.gz
StartedAt: 2019-04-08 22:37:48 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:41:39 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 230.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: adSplit.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:adSplit.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings adSplit_1.53.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/adSplit.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.53.0’
* 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 ... WARNING
Found the following significant warnings:
  adSplit.cpp:256:77: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  adSplit.cpp:469:67: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/adSplit.Rcheck/00install.out’ for details.
* 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 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
drawRandomPS      41.770  0.172  41.970
makeEID2PROBESenv 41.228  0.208  41.469
randomDiana2means 38.705  0.156  38.913
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/adSplit.Rcheck/00check.log’
for details.



Installation output

adSplit.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL adSplit
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘adSplit’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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: ISO C++ forbids converting a 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: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
       throw Tomato(__LINE__, "isis() called with unknown function");
                                                                   ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o adSplit.so adSplit.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-adSplit/00new/adSplit/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (adSplit)

Tests output


Example timings

adSplit.Rcheck/adSplit-Ex.timings

nameusersystemelapsed
adSplit2.1730.1513.624
diana2means1.4880.0251.513
drawRandomPS41.770 0.17241.970
golubKEGGSplits0.0020.0000.002
hist.splitSet0.0090.0000.009
image.splitSet0.1280.0080.155
makeEID2PROBESenv41.228 0.20841.469
print.splitSet0.0010.0000.002
randomDiana2means38.705 0.15638.913