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BioC 3.2: CHECK report for adSplit on zin1

This page was generated on 2016-04-23 10:10:28 -0700 (Sat, 23 Apr 2016).

Package 14/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adSplit 1.40.0
Claudio Lottaz
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/adSplit
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: adSplit
Version: 1.40.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings adSplit_1.40.0.tar.gz
StartedAt: 2016-04-22 21:56:04 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 21:59:30 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 205.7 seconds
RetCode: 0
Status:  OK 
CheckDir: adSplit.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings adSplit_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/adSplit.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.40.0’
* 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/9s] 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 ... [112s/121s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
randomDiana2means 34.916  0.207  35.228
makeEID2PROBESenv 34.394  0.280  36.647
drawRandomPS      33.553  0.212  39.802
* 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-3.2-bioc/meat/adSplit.Rcheck/00check.log’
for details.


adSplit.Rcheck/00install.out:

* installing *source* package ‘adSplit’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -L/usr/local/lib -o adSplit.so adSplit.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)

adSplit.Rcheck/adSplit-Ex.timings:

nameusersystemelapsed
adSplit2.6030.0883.489
diana2means1.4090.0281.441
drawRandomPS33.553 0.21239.802
golubKEGGSplits0.0000.0040.002
hist.splitSet0.0050.0000.006
image.splitSet0.1360.0000.151
makeEID2PROBESenv34.394 0.28036.647
print.splitSet0.0030.0000.002
randomDiana2means34.916 0.20735.228