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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4902
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4692
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4638
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 lconway

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: 2025-11-03 22:15:48 -0500 (Mon, 03 Nov 2025)

EndedAt: 2025-11-03 22:19:50 -0500 (Mon, 03 Nov 2025)

EllapsedTime: 241.9 seconds

RetCode: 1

Status: ERROR

CheckDir: matter.Rcheck

Warnings: NA

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_2.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/matter.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 8.088  0.105   8.226
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6.         └─BiocParallel:::.bpinit(...)
    7.           ├─BiocParallel::bploop(...)
    8.           └─BiocParallel:::bploop.lapply(...)
    9.             └─BiocParallel:::.bploop_impl(...)
   10.               ├─BiocParallel::.manager_send(manager, task)
   11.               └─BiocParallel::.manager_send(manager, task)
   12.                 ├─BiocParallel::.send_to(manager$backend, as.integer(worker), value)
   13.                 └─BiocParallel::.send_to(manager$backend, as.integer(worker), value)
   14.                   ├─parallel:::sendData(backend[[node]], value)
   15.                   └─parallel:::sendData.SOCK0node(backend[[node]], value)
   16.                     └─base::serialize(data, node$con, xdr = FALSE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2076 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 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.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 2076 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-parallel.R:125:2'): SnowfastParam ──────────────────────────────
Error in `serialize(data, node$con, xdr = FALSE)`: error writing to connection
Backtrace:
     ▆
  1. └─matter::chunkLapply(x, sum, BPPARAM = sp0) at test-parallel.R:125:9
  2.   └─matter::chunk_lapply(X, CHUNKFUN, ..., verbose = verbose, BPPARAM = BPPARAM)
  3.     └─matter:::bplapply_int(CHUNKS, CHUNKFUN, ..., BPPARAM = BPPARAM)
  4.       ├─BiocParallel::bplapply(X, FUN, ..., BPPARAM = BPPARAM)
  5.       └─BiocParallel::bplapply(X, FUN, ..., BPPARAM = BPPARAM)
  6.         └─BiocParallel:::.bpinit(...)
  7.           ├─BiocParallel::bploop(...)
  8.           └─BiocParallel:::bploop.lapply(...)
  9.             └─BiocParallel:::.bploop_impl(...)
 10.               ├─BiocParallel::.manager_send(manager, task)
 11.               └─BiocParallel::.manager_send(manager, task)
 12.                 ├─BiocParallel::.send_to(manager$backend, as.integer(worker), value)
 13.                 └─BiocParallel::.send_to(manager$backend, as.integer(worker), value)
 14.                   ├─parallel:::sendData(backend[[node]], value)
 15.                   └─parallel:::sendData.SOCK0node(backend[[node]], value)
 16.                     └─base::serialize(data, node$con, xdr = FALSE)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 2076 ]
Error: Test failures
Execution halted

Example timings

matter.Rcheck/matter-Ex.timings

name	user	system	elapsed
RNGStreams	0.880	0.007	0.903
SnowfastParam-class	0.231	0.027	3.099
approx1	0.002	0.000	0.004
approx2	0.005	0.001	0.006
avg	0.001	0.001	0.002
binpeaks	0.005	0.001	0.007
binvec	0.001	0.001	0.001
bsearch	0.001	0.001	0.002
checksum	0.034	0.007	0.044
chunkApply	0.228	0.019	0.249
chunked-class	0.006	0.001	0.007
colscale	0.263	0.007	0.271
colsweep	0.021	0.001	0.022
convolve_at	0.097	0.005	0.102
coscore	0.044	0.009	0.052
cpal	0.004	0.001	0.004
cv_do	0.186	0.003	0.190
deferred-ops	0.412	0.011	0.428
downsample	0.045	0.002	0.047
drle-class	0.002	0.000	0.003
enhance	0.028	0.003	0.032
estbase	0.012	0.002	0.015
estdim	0.004	0.001	0.004
estnoise	0.038	0.005	0.042
estres	0.002	0.000	0.003
fastmap	0.140	0.002	0.142
fetch	0.162	0.012	0.175
filt1	0.026	0.002	0.028
filt2	0.022	0.001	0.024
filtn	0.004	0.001	0.006
findpeaks	0.027	0.005	0.032
findpeaks_cwt	0.115	0.011	0.129
findpeaks_knn	0.002	0.000	0.003
iQuote	0.001	0.000	0.001
inpoly	0.005	0.001	0.006
isofun	0.029	0.001	0.030
knnsearch	0.001	0.001	0.002
matter-class	0.032	0.003	0.036
matter_arr-class	0.031	0.002	0.034
matter_fct-class	0.019	0.001	0.021
matter_list-class	0.012	0.002	0.013
matter_str-class	0.019	0.002	0.021
mem	0.434	0.009	0.446
mi_learn	0.639	0.010	0.653
nnmf	0.047	0.001	0.048
nscentroids	0.114	0.001	0.116
peakwidths	0.001	0.000	0.001
pinv	0.001	0.000	0.002
plot_signal	0.476	0.055	0.537
pls	0.041	0.001	0.042
prcomp	0.157	0.016	0.175
predscore	0.002	0.000	0.001
rescale	0.001	0.001	0.000
rocscore	0.002	0.001	0.003
rollvec	0.001	0.001	0.002
rowDists	0.097	0.005	0.103
rowStats	0.119	0.009	0.129
seq_rel	0.001	0.001	0.002
sgmix	8.088	0.105	8.226
shingles	0.002	0.002	0.004
simple_logger-class	0.004	0.002	0.007
simspec	0.034	0.007	0.042
sparse_arr-class	0.005	0.001	0.006
stream_stat	0.006	0.001	0.007
struct	0.007	0.002	0.008
summary-stats	0.542	0.023	0.569
to_raster	0.004	0.001	0.004
trans2d	0.044	0.002	0.046
uuid	0.001	0.000	0.001
vizi-functions	0.064	0.006	0.070
warp1	0.030	0.004	0.033
warp2	0.889	0.012	0.905