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BioC 3.4: CHECK report for adSplit on morelia

This page was generated on 2016-09-21 03:49:30 -0700 (Wed, 21 Sep 2016).

Package 14/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adSplit 1.43.0
Claudio Lottaz
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/adSplit
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: adSplit
Version: 1.43.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings adSplit_1.43.0.tar.gz
StartedAt: 2016-09-20 02:52:21 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 02:55:23 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 181.9 seconds
RetCode: 0
Status:  OK 
CheckDir: adSplit.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings adSplit_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/adSplit.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adSplit/DESCRIPTION’ ... OK
* this is package ‘adSplit’ version ‘1.43.0’
* 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 ... NOTE
File ‘adSplit/libs/adSplit.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘adSplit.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... 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 36.431  0.510  39.845
randomDiana2means 29.443  0.414  29.874
drawRandomPS      25.592  0.391  25.988
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/adSplit.Rcheck/00check.log’
for details.


adSplit.Rcheck/00install.out:

* installing *source* package ‘adSplit’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c adSplit.cpp -o adSplit.o
adSplit.cpp:256:28: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
    throw Tomato(__LINE__, "tscore: internal error, shame on the programmer");
                           ^
adSplit.cpp:469:30: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
      throw Tomato(__LINE__, "isis() called with unknown function");
                             ^
2 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o adSplit.so adSplit.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-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
adSplit2.3560.1872.998
diana2means1.2940.0621.685
drawRandomPS25.592 0.39125.988
golubKEGGSplits0.0020.0000.002
hist.splitSet0.0050.0010.006
image.splitSet0.1340.0150.216
makeEID2PROBESenv36.431 0.51039.845
print.splitSet0.0030.0010.003
randomDiana2means29.443 0.41429.874