Package: matter

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:matter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings matter_1.12.0.tar.gz

StartedAt: 2020-04-15 03:34:56 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:36:42 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 106.2 seconds

RetCode: 0

Status:  OK

CheckDir: matter.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:matter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings matter_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/matter.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matter’ version ‘1.12.0’
* 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 ‘matter’ 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/matter.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 matter
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘matter’ ...
** 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 altrep.cpp -o altrep.o
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 bsearch.cpp -o bsearch.o
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 init.cpp -o init.o
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 matter.cpp -o matter.o
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 utils.cpp -o utils.o
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 vectools.cpp -o vectools.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 matter.so altrep.o bsearch.o init.o matter.o utils.o vectools.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-matter/00new/matter/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘apply’ in package ‘matter’
Creating a new generic function for ‘scale’ in package ‘matter’
Creating a new generic function for ‘biglm’ in package ‘matter’
** 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 (matter)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(matter)
Loading required package: BiocParallel
Loading required package: biglm
Loading required package: DBI

Attaching package: 'matter'

The following object is masked from 'package:biglm':

    biglm

The following objects are masked from 'package:base':

    apply, scale

> 
> test_check("matter")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 330 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  7.494   0.480   8.059 

name	user	system	elapsed
apply	0.556	0.016	0.583
biglm	0.044	0.003	0.048
binvec	0.002	0.000	0.002
bsearch	0.000	0.000	0.001
checksum	0.016	0.001	0.017
chunk_apply	0.183	0.017	0.203
colStats	0.018	0.003	0.021
combine-method	0.002	0.000	0.002
combiner-method	0.016	0.000	0.017
delayed-ops	0.011	0.001	0.013
drle-class	0.001	0.000	0.001
keys-method	0.010	0.001	0.011
lapply	0.034	0.001	0.035
locmax	0.001	0.000	0.000
matter-class	0.033	0.002	0.036
matter_arr-class	0.023	0.002	0.024
matter_df-class	0.091	0.005	0.097
matter_fc-class	0.025	0.000	0.025
matter_list-class	0.021	0.001	0.022
matter_mat-class	0.012	0.001	0.014
matter_str-class	0.010	0.003	0.013
matter_vec-class	0.004	0.001	0.005
prcomp	0.030	0.006	0.035
profmem	0.410	0.005	0.417
rep_vt	0.003	0.001	0.004
scale	0.012	0.001	0.013
sparse_mat-class	0.007	0.001	0.008
stream-stats	0.008	0.001	0.008
struct	0.007	0.001	0.008
summary-stats	0.011	0.001	0.012
tolerance-method	0.006	0.001	0.007
uuid	0.001	0.000	0.002
virtual_mat-class	0.006	0.001	0.007