Multiple platform build/check report for BioC 3.22 - CHECK results for matter on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4878
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4624
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4669
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: 2.12.0

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_2.12.0.tar.gz

StartedAt: 2025-12-02 07:27:49 -0500 (Tue, 02 Dec 2025)

EndedAt: 2025-12-02 07:36:42 -0500 (Tue, 02 Dec 2025)

EllapsedTime: 533.5 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_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/matter.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘2.12.0’
* 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: ‘MacOSX11.3.1.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
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
sgmix               21.287  0.150  22.261
SnowfastParam-class  0.510  0.054   5.744
* 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-3.22-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-x86_64/Resources/library’
* installing *source* package ‘matter’ ...
** this is package ‘matter’ version ‘2.12.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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/4.5-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
installing to /Library/Frameworks/R.framework/Versions/4.5-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |====                                                                  |   5%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==========                                                            |  15%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |========================                                              |  35%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |================================                                      |  45%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================                                |  55%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |==============================================                        |  65%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |============================================================          |  85%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |==================================================================    |  95%
  |                                                                            
  |======================================================================| 100%

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2079 ]
> 
> proc.time()
   user  system elapsed 
228.853   7.000 283.749

Example timings

matter.Rcheck/matter-Ex.timings

name	user	system	elapsed
RNGStreams	0.989	0.009	1.005
SnowfastParam-class	0.510	0.054	5.744
approx1	0.003	0.001	0.004
approx2	0.007	0.002	0.010
avg	0.003	0.001	0.004
binpeaks	0.011	0.002	0.012
binvec	0.002	0.001	0.002
bsearch	0.002	0.001	0.003
checksum	0.060	0.011	0.075
chunkApply	0.453	0.036	0.497
chunked-class	0.014	0.004	0.019
colscale	0.577	0.010	0.611
colsweep	0.048	0.002	0.054
convolve_at	0.247	0.010	0.271
coscore	0.083	0.016	0.104
cpal	0.006	0.000	0.007
cv_do	0.402	0.004	0.429
deferred-ops	0.931	0.021	1.006
downsample	0.067	0.004	0.076
drle-class	0.002	0.001	0.005
enhance	0.041	0.004	0.048
estbase	0.016	0.003	0.021
estdim	0.006	0.001	0.007
estnoise	0.058	0.008	0.070
estres	0.002	0.000	0.003
fastmap	0.304	0.003	0.325
fetch	0.338	0.018	0.383
filt1	0.036	0.004	0.043
filt2	0.040	0.003	0.045
filtn	0.007	0.002	0.009
findpeaks	0.044	0.008	0.057
findpeaks_cwt	0.206	0.018	0.230
findpeaks_knn	0.005	0.001	0.006
iQuote	0.001	0.001	0.001
inpoly	0.007	0.002	0.011
isofun	0.053	0.003	0.059
knnsearch	0.002	0.000	0.003
matter-class	0.059	0.005	0.065
matter_arr-class	0.047	0.004	0.053
matter_fct-class	0.040	0.002	0.044
matter_list-class	0.021	0.003	0.025
matter_str-class	0.039	0.004	0.046
mem	0.497	0.013	0.537
mi_learn	1.338	0.015	1.411
nnmf	0.094	0.001	0.102
nscentroids	0.227	0.002	0.240
peakwidths	0.002	0.001	0.004
pinv	0.002	0.002	0.005
plot_signal	0.803	0.064	0.897
pls	0.101	0.001	0.108
prcomp	0.341	0.020	0.401
predscore	0.002	0.000	0.003
rescale	0.001	0.001	0.001
rocscore	0.006	0.002	0.010
rollvec	0.002	0.001	0.002
rowDists	0.200	0.010	0.231
rowStats	0.267	0.014	0.314
seq_rel	0.002	0.004	0.006
sgmix	21.287	0.150	22.261
shingles	0.004	0.004	0.007
simple_logger-class	0.010	0.003	0.013
simspec	0.061	0.011	0.075
sparse_arr-class	0.015	0.003	0.017
stream_stat	0.010	0.002	0.014
struct	0.014	0.002	0.017
summary-stats	1.202	0.029	1.285
to_raster	0.007	0.003	0.010
trans2d	0.069	0.004	0.078
uuid	0.002	0.001	0.003
vizi-functions	0.107	0.009	0.119
warp1	0.059	0.005	0.068
warp2	1.503	0.018	1.611