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"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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: 2024-12-20 05:31:24 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 05:39:31 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 487.6 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               7.165  0.071   7.512
SnowfastParam-class 0.518  0.055   5.701
* 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 7 | PASS 2044 ]

══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• empty test (7): 'test-vizi.R:256:1', 'test-vizi.R:296:1',
  'test-vizi.R:316:1', 'test-vizi.R:337:1', 'test-vizi.R:364:1',
  'test-vizi.R:424:1', 'test-vizi.R:467:1'

[ FAIL 0 | WARN 0 | SKIP 7 | PASS 2044 ]
> 
> proc.time()
   user  system elapsed 
199.804   7.285 254.622

Example timings

matter.Rcheck/matter-Ex.timings

name	user	system	elapsed
RNGStreams	1.016	0.009	1.040
SnowfastParam-class	0.518	0.055	5.701
approx1	0.004	0.001	0.005
approx2	0.007	0.003	0.011
avg	0.004	0.001	0.005
binpeaks	0.011	0.002	0.014
binvec	0.001	0.001	0.002
bsearch	0.002	0.001	0.003
checksum	0.059	0.012	0.072
chunkApply	0.454	0.032	0.533
chunked-class	0.016	0.003	0.029
colscale	0.409	0.007	0.435
colsweep	0.051	0.002	0.055
convolve_at	0.254	0.011	0.269
coscore	0.089	0.015	0.106
cpal	0.006	0.001	0.007
cv_do	0.410	0.004	0.459
deferred-ops	0.575	0.024	0.643
downsample	0.069	0.003	0.074
drle-class	0.003	0.001	0.003
enhance	0.040	0.004	0.046
estbase	0.017	0.003	0.020
estdim	0.005	0.001	0.007
estnoise	0.059	0.007	0.067
estres	0.002	0.001	0.003
fastmap	0.300	0.003	0.318
fetch	0.247	0.016	0.270
filt1	0.049	0.006	0.055
filt2	0.039	0.003	0.041
filtn	0.008	0.002	0.010
findpeaks	0.044	0.008	0.053
findpeaks_cwt	0.225	0.023	0.251
findpeaks_knn	0.005	0.001	0.006
iQuote	0.001	0.000	0.001
inpoly	0.008	0.002	0.010
isofun	0.054	0.003	0.057
knnsearch	0.002	0.001	0.003
matter-class	0.056	0.005	0.061
matter_arr-class	0.049	0.004	0.053
matter_fct-class	0.038	0.002	0.041
matter_list-class	0.020	0.003	0.023
matter_str-class	0.050	0.004	0.058
mem	0.480	0.008	0.494
mi_learn	1.360	0.018	1.403
nnmf	0.097	0.002	0.099
nscentroids	0.226	0.002	0.230
peakwidths	0.002	0.001	0.003
pinv	0.002	0.002	0.005
plot_signal	0.813	0.076	0.899
pls	0.103	0.001	0.106
prcomp	0.243	0.019	0.264
predscore	0.002	0.000	0.003
rescale	0.001	0.001	0.002
rocscore	0.007	0.003	0.009
rollvec	0.002	0.000	0.003
rowDists	0.203	0.010	0.215
rowStats	0.271	0.022	0.294
seq_rel	0.002	0.004	0.007
sgmix	7.165	0.071	7.512
shingles	0.004	0.004	0.008
simple_logger-class	0.010	0.003	0.013
simspec	0.056	0.007	0.065
sparse_arr-class	0.014	0.002	0.016
stream_stat	0.010	0.002	0.013
struct	0.014	0.002	0.018
summary-stats	0.842	0.027	0.930
to_raster	0.007	0.003	0.011
trans2d	0.070	0.005	0.081
uuid	0.002	0.001	0.002
vizi-functions	0.106	0.007	0.118
warp1	0.066	0.006	0.076
warp2	1.510	0.017	1.611