Multiple platform build/check report for BioC 3.21 - CHECK results for matter on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4742
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4459
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 kjohnson3

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: 2.9.1

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_2.9.1.tar.gz

StartedAt: 2025-03-18 20:05:24 -0400 (Tue, 18 Mar 2025)

EndedAt: 2025-03-18 20:06:38 -0400 (Tue, 18 Mar 2025)

EllapsedTime: 73.8 seconds

RetCode: 0

Status: OK

CheckDir: matter.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/matter.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘2.9.1’
* 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-1500.1.0.2.5)’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SnowfastParam-class.Rd: SnowParam, BiocParallelParam, MulticoreParam
  checksum.Rd: digest
  chunkApply.Rd: bplapply
  colscale.Rd: bplapply
  cv_do.Rd: bplapply
  matter-options.Rd: bplapply
  nscentroids.Rd: bplapply
  pls.Rd: bplapply
  prcomp.Rd: bplapply
  rowDists.Rd: bplapply
  rowStats.Rd: bplapply
  sgmix.Rd: bplapply
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
File ‘matter/libs/matter.so’:
  Found non-API calls to R: ‘DATAPTR’, ‘R_tryWrap’, ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/library’
* installing *source* package ‘matter’ ...
** this is package ‘matter’ version ‘2.9.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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/4.5-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/4.5-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/4.5-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/4.5-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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 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 
 26.162   2.046  35.194

Example timings

matter.Rcheck/matter-Ex.timings

name	user	system	elapsed
RNGStreams	0.367	0.001	0.370
SnowfastParam-class	0.068	0.011	0.969
approx1	0.000	0.000	0.001
approx2	0.002	0.000	0.002
avg	0.000	0.000	0.001
binpeaks	0.002	0.000	0.002
binvec	0.001	0.000	0.000
bsearch	0	0	0
checksum	0.009	0.001	0.011
chunkApply	0.072	0.004	0.075
chunked-class	0.002	0.000	0.002
colscale	0.053	0.002	0.055
colsweep	0.007	0.000	0.006
convolve_at	0.025	0.001	0.028
coscore	0.017	0.002	0.019
cpal	0.001	0.000	0.001
cv_do	0.050	0.001	0.051
deferred-ops	0.068	0.003	0.071
downsample	0.015	0.001	0.016
drle-class	0.001	0.000	0.001
enhance	0.009	0.001	0.010
estbase	0.004	0.001	0.005
estdim	0.001	0.000	0.001
estnoise	0.013	0.001	0.014
estres	0.000	0.000	0.001
fastmap	0.034	0.001	0.035
fetch	0.032	0.003	0.035
filt1	0.011	0.001	0.012
filt2	0.011	0.000	0.012
filtn	0.001	0.000	0.002
findpeaks	0.010	0.001	0.012
findpeaks_cwt	0.046	0.004	0.051
findpeaks_knn	0.000	0.001	0.002
iQuote	0	0	0
inpoly	0.001	0.000	0.002
isofun	0.007	0.000	0.007
knnsearch	0.001	0.000	0.001
matter-class	0.007	0.001	0.008
matter_arr-class	0.009	0.001	0.011
matter_fct-class	0.005	0.000	0.006
matter_list-class	0.003	0.000	0.004
matter_str-class	0.006	0.001	0.007
mem	0.189	0.005	0.194
mi_learn	0.160	0.003	0.163
nnmf	0.011	0.000	0.012
nscentroids	0.026	0.000	0.026
peakwidths	0.000	0.001	0.000
pinv	0.000	0.000	0.001
plot_signal	0.163	0.017	0.180
pls	0.013	0.000	0.012
prcomp	0.028	0.004	0.033
predscore	0.001	0.001	0.000
rescale	0	0	0
rocscore	0.001	0.000	0.001
rollvec	0	0	0
rowDists	0.027	0.003	0.029
rowStats	0.032	0.004	0.037
seq_rel	0.000	0.000	0.001
sgmix	0.755	0.023	0.777
shingles	0.000	0.000	0.001
simple_logger-class	0.002	0.001	0.002
simspec	0.014	0.002	0.016
sparse_arr-class	0.002	0.000	0.003
stream_stat	0.002	0.000	0.002
struct	0.002	0.000	0.002
summary-stats	0.091	0.003	0.095
to_raster	0.001	0.000	0.001
trans2d	0.020	0.000	0.021
uuid	0.000	0.000	0.001
vizi-functions	0.017	0.001	0.018
warp1	0.011	0.001	0.013
warp2	0.314	0.003	0.316