Multiple platform build/check report for BioC 3.22 - CHECK results for matter on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
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: 2.11.1

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_2.11.1.tar.gz

StartedAt: 2025-08-08 20:07:48 -0400 (Fri, 08 Aug 2025)

EndedAt: 2025-08-08 20:09:08 -0400 (Fri, 08 Aug 2025)

EllapsedTime: 80.0 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_2.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/matter.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    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 ‘2.11.1’
* 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-3.22-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-arm64/Resources/library’
* installing *source* package ‘matter’ ...
** this is package ‘matter’ version ‘2.11.1’
** 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
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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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")

  |                                                                            
  |                                                                      |   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 
 30.415   1.808  38.882

Example timings

matter.Rcheck/matter-Ex.timings

name	user	system	elapsed
RNGStreams	0.398	0.002	0.401
SnowfastParam-class	0.069	0.010	0.970
approx1	0.000	0.000	0.001
approx2	0.001	0.000	0.001
avg	0	0	0
binpeaks	0.002	0.000	0.002
binvec	0.001	0.000	0.000
bsearch	0.000	0.000	0.001
checksum	0.008	0.002	0.011
chunkApply	0.077	0.005	0.082
chunked-class	0.002	0.000	0.002
colscale	0.076	0.002	0.078
colsweep	0.007	0.000	0.007
convolve_at	0.026	0.002	0.028
coscore	0.015	0.004	0.020
cpal	0.001	0.000	0.001
cv_do	0.051	0.001	0.053
deferred-ops	0.104	0.004	0.108
downsample	0.015	0.000	0.015
drle-class	0	0	0
enhance	0.01	0.00	0.01
estbase	0.004	0.000	0.005
estdim	0.001	0.000	0.002
estnoise	0.014	0.001	0.014
estres	0.000	0.001	0.001
fastmap	0.04	0.00	0.04
fetch	0.042	0.004	0.046
filt1	0.011	0.001	0.012
filt2	0.012	0.000	0.012
filtn	0.001	0.000	0.001
findpeaks	0.011	0.001	0.011
findpeaks_cwt	0.038	0.004	0.042
findpeaks_knn	0.001	0.001	0.002
iQuote	0	0	0
inpoly	0.002	0.000	0.002
isofun	0.008	0.001	0.009
knnsearch	0.001	0.000	0.001
matter-class	0.008	0.001	0.009
matter_arr-class	0.010	0.001	0.010
matter_fct-class	0.006	0.000	0.006
matter_list-class	0.003	0.001	0.004
matter_str-class	0.005	0.001	0.006
mem	0.221	0.004	0.225
mi_learn	0.181	0.005	0.186
nnmf	0.011	0.000	0.012
nscentroids	0.032	0.000	0.033
peakwidths	0.000	0.001	0.000
pinv	0.001	0.000	0.000
plot_signal	0.175	0.022	0.197
pls	0.014	0.000	0.014
prcomp	0.040	0.004	0.045
predscore	0.001	0.000	0.001
rescale	0	0	0
rocscore	0.001	0.000	0.001
rollvec	0	0	0
rowDists	0.028	0.002	0.030
rowStats	0.031	0.003	0.042
seq_rel	0.000	0.001	0.001
sgmix	2.434	0.058	2.502
shingles	0.001	0.001	0.002
simple_logger-class	0.002	0.001	0.002
simspec	0.013	0.001	0.016
sparse_arr-class	0.002	0.000	0.003
stream_stat	0.001	0.001	0.002
struct	0.002	0.000	0.003
summary-stats	0.142	0.006	0.147
to_raster	0.001	0.001	0.001
trans2d	0.020	0.000	0.021
uuid	0	0	0
vizi-functions	0.018	0.002	0.020
warp1	0.012	0.001	0.012
warp2	0.321	0.005	0.327