##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:matter.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings matter_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/matter.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.22.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/matter/libs/x64/matter.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... WARNING
Found the following significant warnings:

  Warning: 'default.stringsAsFactors' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/matter.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL matter
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'matter' ...
** using staged installation
** libs
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c altrep.cpp -o altrep.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bsearch.cpp -o bsearch.o
bsearch.cpp: In function 'size_t binary_search(T, SEXP, size_t, size_t, double, int, int, bool) [with T = const char*]':
bsearch.cpp:51:36: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized]
   51 |   else if ( mid == right && result > 0 )
      |                             ~~~~~~~^~~
bsearch.cpp: In function 'size_t binary_search(T, SEXP, size_t, size_t, double, int, int, bool) [with T = double]':
bsearch.cpp:136:27: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
  136 |   else if ( (mid == right && diff > 0) && (nearest || dright < tol) )
      |             ~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.cpp -o init.o
In file included from init.cpp:5:
altrep.h:20:25: warning: 'MatterAlt_string' defined but not used [-Wunused-variable]
   20 | static R_altrep_class_t MatterAlt_string;
      |                         ^~~~~~~~~~~~~~~~
altrep.h:19:25: warning: 'MatterAlt_real' defined but not used [-Wunused-variable]
   19 | static R_altrep_class_t MatterAlt_real;
      |                         ^~~~~~~~~~~~~~
altrep.h:18:25: warning: 'MatterAlt_integer' defined but not used [-Wunused-variable]
   18 | static R_altrep_class_t MatterAlt_integer;
      |                         ^~~~~~~~~~~~~~~~~
altrep.h:17:25: warning: 'MatterAlt_logical' defined but not used [-Wunused-variable]
   17 | static R_altrep_class_t MatterAlt_logical;
      |                         ^~~~~~~~~~~~~~~~~
altrep.h:16:25: warning: 'MatterAlt_raw' defined but not used [-Wunused-variable]
   16 | static R_altrep_class_t MatterAlt_raw;
      |                         ^~~~~~~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matter.cpp -o matter.o
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = double]':
matter.cpp:3409:33: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
 3409 |                         add<T,T>(x, y, i, atm, 0, count, skip);
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = int]':
matter.cpp:3409:33: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
 3409 |                         add<T,T>(x, y, i, atm, 0, count, skip);
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = unsigned char]':
matter.cpp:1147:28: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1147 |                     tmp = y[atm->group()];
      |                           ~^
matter.cpp:3389:13: note: 'y' was declared here
 3389 |         T * y;
      |             ^
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vectools.cpp -o vectools.o
g++ -std=gnu++11 -shared -s -static-libgcc -o matter.dll tmp.def altrep.o bsearch.o init.o matter.o utils.o vectools.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-matter/00new/matter/libs/x64
** 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
** 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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: Matrix
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")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 343 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 343 ]
> 
> proc.time()
   user  system elapsed 
   9.50    1.23   11.32