Multiple platform build/check report for BioC 3.20 - CHECK results for matter on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4493
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4394
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*

CHECK results for matter on kjohnson1

To the developers/maintainers of the matter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/matter.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: matter

Version: 2.8.0

Command: /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_2.8.0.tar.gz

StartedAt: 2025-01-22 00:06:11 -0500 (Wed, 22 Jan 2025)

EndedAt: 2025-01-22 00:09:49 -0500 (Wed, 22 Jan 2025)

EllapsedTime: 218.2 seconds

RetCode: 0

Status: OK

CheckDir: matter.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /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_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/matter.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matter’ version ‘2.8.0’
* 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
* 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 code 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 whether 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 ... 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-3.20-bioc/meat/matter.Rcheck/00check.log’
for details.

Installation output

matter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL matter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c init.cpp -o init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c matterExports.cpp -o matterExports.o
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/4.4-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

matter.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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")

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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2079 ]
> 
> proc.time()
   user  system elapsed 
 82.381   5.446 106.947

Example timings

matter.Rcheck/matter-Ex.timings

name	user	system	elapsed
RNGStreams	1.015	0.005	1.021
SnowfastParam-class	0.217	0.035	3.105
approx1	0.002	0.001	0.005
approx2	0.005	0.002	0.006
avg	0.002	0.001	0.002
binpeaks	0.007	0.001	0.007
binvec	0.001	0.000	0.001
bsearch	0.001	0.000	0.002
checksum	0.030	0.006	0.045
chunkApply	0.229	0.013	0.242
chunked-class	0.007	0.001	0.008
colscale	0.186	0.007	0.193
colsweep	0.021	0.001	0.023
convolve_at	0.082	0.005	0.088
coscore	0.050	0.007	0.057
cpal	0.004	0.000	0.004
cv_do	0.169	0.003	0.172
deferred-ops	0.210	0.011	0.221
downsample	0.048	0.002	0.050
drle-class	0.002	0.000	0.001
enhance	0.029	0.002	0.032
estbase	0.014	0.001	0.017
estdim	0.003	0.000	0.003
estnoise	0.043	0.004	0.047
estres	0.002	0.000	0.001
fastmap	0.122	0.001	0.123
fetch	0.10	0.01	0.11
filt1	0.045	0.004	0.048
filt2	0.037	0.001	0.039
filtn	0.004	0.001	0.005
findpeaks	0.035	0.005	0.039
findpeaks_cwt	0.138	0.013	0.151
findpeaks_knn	0.003	0.000	0.003
iQuote	0.001	0.000	0.001
inpoly	0.003	0.001	0.004
isofun	0.022	0.001	0.024
knnsearch	0.001	0.000	0.001
matter-class	0.025	0.004	0.030
matter_arr-class	0.029	0.002	0.030
matter_fct-class	0.018	0.002	0.019
matter_list-class	0.010	0.002	0.012
matter_str-class	0.021	0.002	0.022
mem	0.546	0.011	0.558
mi_learn	0.550	0.010	0.561
nnmf	0.035	0.001	0.036
nscentroids	0.091	0.001	0.092
peakwidths	0.001	0.000	0.001
pinv	0.001	0.001	0.002
plot_signal	0.553	0.051	0.615
pls	0.041	0.000	0.042
prcomp	0.091	0.009	0.101
predscore	0.001	0.000	0.001
rescale	0.000	0.001	0.001
rocscore	0.003	0.001	0.003
rollvec	0.001	0.000	0.001
rowDists	0.087	0.005	0.093
rowStats	0.101	0.010	0.111
seq_rel	0.000	0.002	0.002
sgmix	2.372	0.061	2.434
shingles	0.002	0.001	0.003
simple_logger-class	0.005	0.002	0.007
simspec	0.040	0.005	0.045
sparse_arr-class	0.007	0.001	0.008
stream_stat	0.005	0.001	0.006
struct	0.007	0.001	0.008
summary-stats	0.327	0.012	0.340
to_raster	0.002	0.001	0.004
trans2d	0.063	0.002	0.065
uuid	0.001	0.000	0.001
vizi-functions	0.055	0.006	0.060
warp1	0.036	0.003	0.038
warp2	0.988	0.018	1.006