Mac ARM64 build report for BioC 3.18 - CHECK results for matter on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4388
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:matter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings matter_2.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/matter.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matter’ version ‘2.4.1’
* 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
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 startup messages can be suppressed ... 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 compiled code ... NOTE
Note: information on .o files is not available
* 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-3.18-bioc-mac-arm64/meat/matter.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL matter
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘matter’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c altrep.cpp -o altrep.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.cpp -o init.o
In file included from init.cpp:3:
In file included from ./matterExports.h:13:
./signal2.h:153:24: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
        index_t ii, jj, prev, lo, hi;
                              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c matterExports.cpp -o matterExports.o
In file included from matterExports.cpp:2:
In file included from ./matterExports.h:13:
./signal2.h:153:24: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
        index_t ii, jj, prev, lo, hi;
                              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o matter.so altrep.o init.o matterExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-matter/00new/matter/libs
** R
** byte-compile and prepare package for lazy loading
** 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)

Tests output


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
> 
> test_check("matter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1349 ]
> 
> proc.time()
   user  system elapsed 
 33.831   1.564  35.744

Example timings

name	user	system	elapsed
approx1	0.003	0.001	0.006
approx2	0.006	0.001	0.008
asearch	0.001	0.000	0.001
biglm	0.097	0.005	0.103
binpeaks	0.006	0.000	0.007
binvec	0.001	0.000	0.001
bsearch	0.001	0.001	0.001
checksum	0.018	0.002	0.024
chunkApply	1.270	0.015	1.296
colscale	0.088	0.004	0.092
colsweep	0.012	0.001	0.014
convolve_at	0.090	0.009	0.100
cpal	0.003	0.000	0.003
deferred-ops	0.041	0.004	0.045
downsample	0.032	0.003	0.035
drle-class	0.000	0.000	0.001
enhance	0.013	0.003	0.017
estbase	0.006	0.002	0.007
estdim	0.002	0.000	0.002
estnoise	0.044	0.004	0.050
estres	0	0	0
fastmap	0.120	0.011	0.137
filt1	0.012	0.003	0.015
filt2	0.014	0.002	0.016
findpeaks	0.019	0.005	0.025
findpeaks_cwt	0.055	0.011	0.067
image	0.153	0.017	0.170
inpoly	0.004	0.000	0.005
knnsearch	0.001	0.000	0.001
matter-class	0.022	0.003	0.024
matter_arr-class	0.030	0.002	0.036
matter_fct-class	0.010	0.001	0.017
matter_list-class	0.007	0.001	0.009
matter_str-class	0.008	0.002	0.011
memtime	0.553	0.013	0.588
nnmf	0.017	0.001	0.018
peakwidths	0.000	0.000	0.001
pls	0.025	0.000	0.026
prcomp	0.055	0.009	0.067
rollvec	0.001	0.000	0.001
rowDists	0.043	0.001	0.046
rowStats	0.089	0.006	0.097
simspec	0.038	0.007	0.046
sparse_arr-class	0.006	0.001	0.007
stream-stats	0.007	0.001	0.009
struct	0.007	0.001	0.009
summary-stats	0.137	0.017	0.154
to_raster	0.004	0.002	0.005
trans2d	0.058	0.004	0.063
uuid	0.001	0.000	0.002
vizi	0.066	0.009	0.075
warp1	0.035	0.004	0.040
warp2	1.005	0.019	1.044

CHECK results for matter on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings