Multiple platform build/check report for BioC 3.20 - CHECK results for matter on merida1

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 merida1

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: 2025-01-21 06:04:13 -0500 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 06:12:29 -0500 (Tue, 21 Jan 2025)

EllapsedTime: 495.9 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: x86_64-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 Monterey 12.7.6
* 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 14.0.0 (clang-1400.0.29.202)’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
sgmix               7.088  0.074   7.574
SnowfastParam-class 0.513  0.060   5.745
* 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-x86_64/Resources/library’
* installing *source* package ‘matter’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c altrep.cpp -o altrep.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c init.cpp -o init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c matterExports.cpp -o matterExports.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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: x86_64-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 
196.916   7.347 257.699

Example timings

matter.Rcheck/matter-Ex.timings

name	user	system	elapsed
RNGStreams	1.041	0.010	1.084
SnowfastParam-class	0.513	0.060	5.745
approx1	0.003	0.001	0.004
approx2	0.007	0.003	0.010
avg	0.003	0.001	0.004
binpeaks	0.012	0.002	0.016
binvec	0.002	0.001	0.002
bsearch	0.002	0.001	0.004
checksum	0.057	0.010	0.069
chunkApply	0.445	0.034	0.488
chunked-class	0.015	0.004	0.020
colscale	0.404	0.006	0.412
colsweep	0.049	0.002	0.051
convolve_at	0.256	0.008	0.270
coscore	0.090	0.015	0.106
cpal	0.006	0.000	0.007
cv_do	0.404	0.004	0.419
deferred-ops	0.574	0.025	0.603
downsample	0.063	0.004	0.067
drle-class	0.002	0.001	0.004
enhance	0.041	0.005	0.046
estbase	0.017	0.003	0.020
estdim	0.006	0.001	0.007
estnoise	0.059	0.008	0.069
estres	0.003	0.000	0.003
fastmap	0.292	0.002	0.300
fetch	0.248	0.018	0.272
filt1	0.049	0.006	0.061
filt2	0.040	0.002	0.050
filtn	0.008	0.002	0.010
findpeaks	0.044	0.007	0.052
findpeaks_cwt	0.233	0.021	0.263
findpeaks_knn	0.005	0.001	0.006
iQuote	0.001	0.001	0.002
inpoly	0.007	0.002	0.009
isofun	0.055	0.003	0.061
knnsearch	0.003	0.001	0.003
matter-class	0.055	0.006	0.067
matter_arr-class	0.048	0.004	0.055
matter_fct-class	0.040	0.002	0.049
matter_list-class	0.021	0.003	0.032
matter_str-class	0.050	0.005	0.056
mem	0.492	0.012	0.522
mi_learn	1.347	0.028	1.408
nnmf	0.099	0.001	0.104
nscentroids	0.230	0.002	0.235
peakwidths	0.002	0.001	0.003
pinv	0.003	0.003	0.005
plot_signal	0.807	0.088	0.935
pls	0.100	0.002	0.126
prcomp	0.225	0.019	0.248
predscore	0.002	0.001	0.003
rescale	0.001	0.001	0.002
rocscore	0.006	0.002	0.008
rollvec	0.002	0.001	0.002
rowDists	0.194	0.008	0.203
rowStats	0.258	0.022	0.280
seq_rel	0.002	0.004	0.005
sgmix	7.088	0.074	7.574
shingles	0.003	0.003	0.007
simple_logger-class	0.010	0.003	0.013
simspec	0.055	0.007	0.064
sparse_arr-class	0.014	0.003	0.017
stream_stat	0.011	0.003	0.015
struct	0.014	0.003	0.017
summary-stats	0.804	0.021	0.853
to_raster	0.007	0.003	0.011
trans2d	0.068	0.004	0.074
uuid	0.002	0.001	0.003
vizi-functions	0.107	0.010	0.122
warp1	0.062	0.007	0.069
warp2	1.498	0.020	1.646