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CHECK report for adSplit on merida1

This page was generated on 2020-08-13 11:48:21 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE adSplit PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 20/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adSplit 1.59.0
Claudio Lottaz
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/adSplit
Branch: master
Last Commit: 4069672
Last Changed Date: 2020-06-05 04:09:27 -0400 (Fri, 05 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: adSplit
Version: 1.59.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:adSplit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings adSplit_1.59.0.tar.gz
StartedAt: 2020-08-12 22:54:34 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 22:59:34 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 300.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: adSplit.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:adSplit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings adSplit_1.59.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/adSplit.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adSplit/DESCRIPTION’ ... OK
* this is package ‘adSplit’ version ‘1.59.0’
* 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:256:28: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  adSplit.cpp:469:30: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
See ‘/Users/biocbuild/bbs-3.12-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
File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/adSplit/libs/adSplit.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
makeEID2PROBESenv 52.343  0.496  52.912
drawRandomPS      51.949  0.452  52.492
randomDiana2means 50.510  0.489  51.077
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/adSplit.Rcheck/00check.log’
for details.



Installation output

adSplit.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL adSplit
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘adSplit’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c adSplit.cpp -o adSplit.o
adSplit.cpp:256:28: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
    throw Tomato(__LINE__, "tscore: internal error, shame on the programmer");
                           ^
adSplit.cpp:469:30: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
      throw Tomato(__LINE__, "isis() called with unknown function");
                             ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 /Library/Frameworks/R.framework/Versions/4.0/Resources/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
adSplit2.5470.1922.746
diana2means2.0090.0792.091
drawRandomPS51.949 0.45252.492
golubKEGGSplits0.0020.0010.002
hist.splitSet0.0090.0020.010
image.splitSet0.2280.0380.300
makeEID2PROBESenv52.343 0.49652.912
print.splitSet0.0020.0010.003
randomDiana2means50.510 0.48951.077