Multiple platform build/check report for BioC 3.7 - CHECK report for beachmat on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:beachmat.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings beachmat_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/beachmat.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beachmat/DESCRIPTION’ ... OK
* this is package ‘beachmat’ version ‘1.2.1’
* 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 ... NOTE
  installed size is 60.1Mb
  sub-directories of 1Mb or more:
    lib   39.9Mb
    libs  19.7Mb
* 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 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/libs/beachmat.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/beachmat.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL beachmat
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘beachmat’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c HDF5_utils.cpp -o HDF5_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c any_matrix.cpp -o any_matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c character_matrix.cpp -o character_matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c character_output.cpp -o character_output.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c find_chunks.cpp -o find_chunks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c functions.cpp -o functions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c integer_matrix.cpp -o integer_matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c logical_matrix.cpp -o logical_matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c numeric_matrix.cpp -o numeric_matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c output_param.cpp -o output_param.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c repacker.cpp -o repacker.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o beachmat.so HDF5_utils.o any_matrix.o character_matrix.o character_output.o find_chunks.o functions.o integer_matrix.o logical_matrix.o numeric_matrix.o output_param.o repacker.o utils.o /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
ar rc libbeachmat.a any_matrix.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o
g++ -std=gnu++11 -shared -L/usr/local/lib -o libbeachmat.so any_matrix.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o `echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "/home/biocbuild/bbs-3.7-bioc/R/bin/R" --vanilla --slave` 
mkdir -p "/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/lib" "/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat"
cp any_matrix.h utils.h beachmat.h HDF5_utils.h output_param.h Psymm_matrix.h HDF5_matrix.h Csparse_matrix.h dense_matrix.h simple_matrix.h Rle_matrix.h Input_matrix.h delayed_matrix.h delayed_methods.h unknown_matrix.h simple_output.h Csparse_output.h HDF5_output.h Output_matrix.h LIN_matrix.h LIN_methods.h LIN_output.h LIN_outfun.h logical_matrix.h integer_matrix.h character_matrix.h numeric_matrix.h character_output.h   "/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat"
mv libbeachmat.* "/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/lib"
installing to /home/biocbuild/bbs-3.7-bioc/R/library/beachmat/libs
** R
** 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 (beachmat)

Tests output


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(beachmat)
> test_check("beachmat")
* checking for file ‘/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/testpkg/DESCRIPTION’ ... OK
* preparing ‘beachtest’:
* checking DESCRIPTION meta-information ... OK
* 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’

* using log directory ‘/tmp/RtmpTHf8iJ/beachtest.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 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:
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, rx)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, it)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, i)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 0L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 1L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -1L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 2L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -2L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 3L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -3L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 0L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 1L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -1L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 2L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -2L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 3L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -3L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 4L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -4L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 5L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -5L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, 6L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, x, -6L)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, mats[[i]], 1L, NULL)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, rx)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, it, ordering)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, it, c, subr)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, it, r, subc)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, i, ordering)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, it, rx, ry)
  symbol ‘cxxfun’ not in namespace:
   .Call(cxxfun, test.mat, i, rx, ry)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘check_character_const_mat’ ‘check_character_const_slice’
  ‘check_character_edge_errors’ ‘check_character_edge_output_errors’
  ‘check_character_indexed_mat’ ‘check_character_indexed_slice’
  ‘check_character_mat’ ‘check_character_order’
  ‘check_character_output_indexed’ ‘check_character_output_mat’
  ‘check_character_output_slice’ ‘check_character_slice’
  ‘check_integer_const_mat’ ‘check_integer_const_slice’
  ‘check_integer_conversion’ ‘check_integer_converted_output’
  ‘check_integer_edge_errors’ ‘check_integer_edge_output_errors’
  ‘check_integer_indexed_mat’ ‘check_integer_indexed_slice’
  ‘check_integer_mat’ ‘check_integer_order’
  ‘check_integer_output_indexed’ ‘check_integer_output_mat’
  ‘check_integer_output_slice’ ‘check_integer_slice’
  ‘check_logical_const_mat’ ‘check_logical_const_slice’
  ‘check_logical_conversion’ ‘check_logical_converted_output’
  ‘check_logical_edge_errors’ ‘check_logical_edge_output_errors’
  ‘check_logical_indexed_mat’ ‘check_logical_indexed_slice’
  ‘check_logical_mat’ ‘check_logical_order’
  ‘check_logical_output_indexed’ ‘check_logical_output_mat’
  ‘check_logical_output_slice’ ‘check_logical_slice’
  ‘check_numeric_const_mat’ ‘check_numeric_const_slice’
  ‘check_numeric_conversion’ ‘check_numeric_converted_output’
  ‘check_numeric_edge_errors’ ‘check_numeric_edge_output_errors’
  ‘check_numeric_indexed_mat’ ‘check_numeric_indexed_slice’
  ‘check_numeric_mat’ ‘check_numeric_order’
  ‘check_numeric_output_indexed’ ‘check_numeric_output_mat’
  ‘check_numeric_output_slice’ ‘check_numeric_slice’
  ‘check_output_mode’ ‘check_type’ ‘delayed_funs’
All user-level objects in a package 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [65s/65s]
 OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/tmp/RtmpTHf8iJ/beachtest.Rcheck/00check.log’
for details.


══ testthat results  ═══════════════════════════════════════════════════════════
OK: 109 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
131.532   4.760 140.554

name	user	system	elapsed
getBestChunkDims	0.000	0.000	0.001
pkgconfig	0.004	0.000	0.002
rechunkByMargins	0.348	0.000	0.382

CHECK report for beachmat on malbec2

Summary

Command output

Installation output

Tests output

Example timings