Package: diffuStats

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffuStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffuStats_1.2.0.tar.gz

StartedAt: 2019-04-15 23:32:05 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:33:28 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 83.4 seconds

RetCode: 0

Status:  OK

CheckDir: diffuStats.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffuStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffuStats_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/diffuStats.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffuStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘diffuStats’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘diffuStats’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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-3.8-bioc/meat/diffuStats.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 diffuStats
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘diffuStats’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c diffuse_parallel.cpp -o diffuse_parallel.o
diffuse_parallel.cpp:28:48: warning: 'acquire_chunked<double>' is deprecated [-Wdeprecated-declarations]
  arma::access::rw(res.values) = arma::memory::acquire_chunked<double>(x.size() + 1);
                                               ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:9: note: 'acquire_chunked<double>' has been explicitly marked deprecated here
memory::acquire_chunked(const uword n_elem)
        ^
diffuse_parallel.cpp:32:53: warning: 'acquire_chunked<unsigned int>' is deprecated [-Wdeprecated-declarations]
  arma::access::rw(res.row_indices) = arma::memory::acquire_chunked<arma::uword>(i.size() + 1);
                                                    ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:9: note: 'acquire_chunked<unsigned int>' has been explicitly marked deprecated here
memory::acquire_chunked(const uword n_elem)
        ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
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 diffuStats.so RcppExports.o diffuse_parallel.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/diffuStats/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffuStats)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(diffuStats)
> 
> test_check("diffuStats")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 208 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 25.190   1.433  12.439 

name	user	system	elapsed
checks	0.104	0.009	0.117
connect_undirected_graph	0.024	0.002	0.025
diffuse	1.621	0.211	1.602
diffuse_mc	0.311	0.034	0.286
diffuse_raw	0.022	0.001	0.023
generate_graph	0.014	0.000	0.015
generate_input	0.035	0.001	0.036
is_kernel	0.013	0.001	0.013
kernels	0.042	0.002	0.045
largest_cc	0.014	0.000	0.015
metric_auc	0.091	0.001	0.096
named.list	0.000	0.000	0.001
perf	0.337	0.006	0.349
perf_eval	0.071	0.001	0.072
perf_wilcox	0.072	0.001	0.073
scores2colours	0.003	0.001	0.003
scores2shapes	0.000	0.000	0.001
to_list	0.003	0.001	0.004
to_x_from_list	0.002	0.001	0.003
which_format	0.002	0.001	0.004