Package: adSplit

Version: 1.54.0

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_1.54.0.tar.gz

StartedAt: 2019-10-16 00:24:41 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:30:26 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 345.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: adSplit.Rcheck

Warnings: 1

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### Running command:
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###   /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_1.54.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/adSplit.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adSplit/DESCRIPTION’ ... OK
* this is package ‘adSplit’ version ‘1.54.0’
* 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-3.9-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
File ‘/Library/Frameworks/R.framework/Versions/3.6/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 or elapsed time > 5s
                    user system elapsed
randomDiana2means 65.362  0.797  66.246
makeEID2PROBESenv 57.217  0.597  57.830
drawRandomPS      55.285  0.691  55.990
* 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-3.9-bioc/meat/adSplit.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL adSplit
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘adSplit’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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++ -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/3.6/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)

name	user	system	elapsed
adSplit	2.914	0.305	3.241
diana2means	2.302	0.186	2.496
drawRandomPS	55.285	0.691	55.990
golubKEGGSplits	0.002	0.001	0.004
hist.splitSet	0.011	0.002	0.013
image.splitSet	0.223	0.076	0.358
makeEID2PROBESenv	57.217	0.597	57.830
print.splitSet	0.003	0.002	0.006
randomDiana2means	65.362	0.797	66.246