Package: beachmat

Version: 2.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_2.3.1.tar.gz

StartedAt: 2020-01-11 11:00:44 -0500 (Sat, 11 Jan 2020)

EndedAt: 2020-01-11 11:37:54 -0500 (Sat, 11 Jan 2020)

EllapsedTime: 2230.1 seconds

RetCode: 0

Status:  OK

CheckDir: beachmat.Rcheck

Warnings: 0

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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.

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Type 'contributors()' for more information and
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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(beachmat)
> test_check("beachmat")
── Building ─────────────────────────────────────────────────────── beachtest ──
Setting env vars:
● CFLAGS    : -Wall -pedantic
● CXXFLAGS  : -Wall -pedantic
● CXX11FLAGS: -Wall -pedantic
────────────────────────────────────────────────────────────────────────────────
  
   checking for file ‘/Users/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck/beachmat/testpkg/DESCRIPTION’ ...
  
✔  checking for file ‘/Users/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck/beachmat/testpkg/DESCRIPTION’ (560ms)

  
─  preparing ‘beachtest’:

  
   checking DESCRIPTION meta-information ...
  
✔  checking DESCRIPTION meta-information

  
─  cleaning src

  
─  checking for LF line-endings in source and make files and shell scripts

  
─  checking for empty or unneeded directories

  
─  building ‘beachtest_1.0.0.tar.gz’

  
   

── Checking ─────────────────────────────────────────────────────── beachtest ──
Setting env vars:
● _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
● _R_CHECK_CRAN_INCOMING_       : FALSE
● _R_CHECK_FORCE_SUGGESTS_      : FALSE
── R CMD check ─────────────────────────────────────────────────────────────────
* using log directory ‘/private/tmp/RtmpRMl8vd/beachtest.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘beachtest/DESCRIPTION’ ... OK
* this is package ‘beachtest’ version ‘1.0.0’
* 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 serialization versions ... OK
* checking whether package ‘beachtest’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 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 ... NOTE
Registration problems:
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o - 1L, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o - 1L, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, ro, co, PACKAGE = "beachtest")
  Evaluating ‘paste0("get_class_", mode)’ during check gives error
‘cannot coerce type 'closure' to vector of type 'character'’:
   .Call(paste0("get_class_", mode), test.mat, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o - 1L, b, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o - 1L, b, PACKAGE = "beachtest")
  Evaluating ‘paste0("get_row_", mode, "_to_", alt.mode)’ during check gives error
‘object 'alt.mode' not found’:
   .Call(paste0("get_row_", mode, "_to_", alt.mode), test.mat, ordering, 
       PACKAGE = "beachtest")
  Evaluating ‘paste0("get_col_", mode, "_to_", alt.mode)’ during check gives error
‘object 'alt.mode' not found’:
   .Call(paste0("get_col_", mode, "_to_", alt.mode), test.mat, ordering, 
       PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, rbounds, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, cbounds, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, ro, co, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, subr)
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, subr)
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
  Evaluating ‘paste0("set_row_", mode, "_via_", alt.mode)’ during check gives error
‘object 'alt.mode' not found’:
   .Call(paste0("set_row_", mode, "_via_", alt.mode), test.mat, 
       ordering, PACKAGE = "beachtest")
  Evaluating ‘paste0("set_col_", mode, "_via_", alt.mode)’ during check gives error
‘object 'alt.mode' not found’:
   .Call(paste0("set_col_", mode, "_via_", alt.mode), test.mat, 
       ordering, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, rbounds, PACKAGE = "beachtest")
  Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
   .Call(paste0(FUN, "_", mode), test.mat, o, cbounds, PACKAGE = "beachtest")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘beachtest/libs/beachtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [15m/15m]
 OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 NOTEs
See
  ‘/private/tmp/RtmpRMl8vd/beachtest.Rcheck/00check.log’
for details.


── Building ─────────────────────────────────────────────────────── morebeach ──
Setting env vars:
● CFLAGS    : -Wall -pedantic
● CXXFLAGS  : -Wall -pedantic
● CXX11FLAGS: -Wall -pedantic
────────────────────────────────────────────────────────────────────────────────
  
   checking for file ‘/Users/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck/beachmat/extensions/DESCRIPTION’ ...
  
✔  checking for file ‘/Users/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck/beachmat/extensions/DESCRIPTION’ (543ms)

  
─  preparing ‘morebeach’:

  
   checking DESCRIPTION meta-information ...
  
✔  checking DESCRIPTION meta-information
─  cleaning src

  
─  checking for LF line-endings in source and make files and shell scripts

  
─  checking for empty or unneeded directories

  
─  building ‘morebeach_1.0.0.tar.gz’

  
   

── Checking ─────────────────────────────────────────────────────── morebeach ──
Setting env vars:
● _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
● _R_CHECK_CRAN_INCOMING_       : FALSE
● _R_CHECK_FORCE_SUGGESTS_      : FALSE
── R CMD check ─────────────────────────────────────────────────────────────────
* using log directory ‘/private/tmp/RtmpRMl8vd/morebeach.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘morebeach/DESCRIPTION’ ... OK
* this is package ‘morebeach’ version ‘1.0.0’
* 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 serialization versions ... OK
* checking whether package ‘morebeach’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
as.matrix:
  function(x, ...)
as.matrix.AaronMatrix:
  function(x)

as.matrix:
  function(x, ...)
as.matrix.AaronMatrix:
  function(x)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘AaronMatrix’
Undocumented S4 classes:
  ‘AaronMatrix’
Undocumented S4 methods:
  generic '[' and siglist 'AaronMatrix,ANY,ANY,ANY'
  generic 'as.matrix' and siglist 'AaronMatrix'
  generic 'dim' and siglist 'AaronMatrix'
  generic 'type' and siglist 'AaronMatrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘morebeach/libs/morebeach.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [472s/471s]
 OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/private/tmp/RtmpRMl8vd/morebeach.Rcheck/00check.log’
for details.


══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
    user   system  elapsed 
2040.394   74.226 2111.467 

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_2.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘beachmat/DESCRIPTION’ ... OK
* this is package ‘beachmat’ version ‘2.3.1’
* 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 ‘beachmat’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 for missing documentation entries ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

* installing *source* package ‘beachmat’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘beachmat’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beachmat)