Multiple platform build/check report for BioC 3.20 - CHECK results for matter on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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: 2.8.0

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: 2024-11-19 23:41:00 -0500 (Tue, 19 Nov 2024)

EndedAt: 2024-11-19 23:47:21 -0500 (Tue, 19 Nov 2024)

EllapsedTime: 381.5 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_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/matter.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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, 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.fail


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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")
[ 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	0.698	0.004	0.702
SnowfastParam-class	0.159	0.025	2.144
approx1	0.001	0.000	0.003
approx2	0.003	0.001	0.004
avg	0.001	0.001	0.002
binpeaks	0.005	0.001	0.005
binvec	0.001	0.001	0.001
bsearch	0.001	0.000	0.001
checksum	0.024	0.005	0.032
chunkApply	0.161	0.014	0.176
chunked-class	0.006	0.001	0.007
colscale	0.139	0.003	0.143
colsweep	0.016	0.000	0.017
convolve_at	0.062	0.003	0.065
coscore	0.034	0.007	0.041
cpal	0.003	0.000	0.003
cv_do	0.132	0.001	0.133
deferred-ops	0.173	0.009	0.182
downsample	0.029	0.001	0.031
drle-class	0.001	0.000	0.001
enhance	0.017	0.002	0.020
estbase	0.008	0.001	0.009
estdim	0.003	0.000	0.002
estnoise	0.026	0.003	0.030
estres	0.002	0.000	0.002
fastmap	0.095	0.001	0.096
fetch	0.082	0.009	0.092
filt1	0.026	0.003	0.031
filt2	0.020	0.001	0.022
filtn	0.003	0.001	0.003
findpeaks	0.019	0.003	0.022
findpeaks_cwt	0.101	0.014	0.116
findpeaks_knn	0.002	0.000	0.003
iQuote	0	0	0
inpoly	0.002	0.001	0.004
isofun	0.019	0.001	0.020
knnsearch	0.001	0.000	0.001
matter-class	0.020	0.002	0.022
matter_arr-class	0.021	0.001	0.022
matter_fct-class	0.014	0.001	0.015
matter_list-class	0.007	0.001	0.009
matter_str-class	0.017	0.001	0.018
mem	0.357	0.006	0.366
mi_learn	0.424	0.007	0.430
nnmf	0.033	0.001	0.034
nscentroids	0.074	0.001	0.075
peakwidths	0.000	0.000	0.001
pinv	0.001	0.000	0.001
plot_signal	0.356	0.063	0.424
pls	0.031	0.000	0.032
prcomp	0.076	0.011	0.086
predscore	0.001	0.000	0.001
rescale	0.001	0.001	0.000
rocscore	0.002	0.001	0.003
rollvec	0.000	0.000	0.002
rowDists	0.067	0.003	0.071
rowStats	0.083	0.012	0.095
seq_rel	0.000	0.001	0.001
sgmix	1.834	0.049	1.890
shingles	0.002	0.001	0.002
simple_logger-class	0.004	0.001	0.006
simspec	0.022	0.003	0.027
sparse_arr-class	0.005	0.001	0.006
stream_stat	0.004	0.001	0.005
struct	0.005	0.001	0.005
summary-stats	0.246	0.012	0.258
to_raster	0.003	0.001	0.003
trans2d	0.034	0.002	0.036
uuid	0.000	0.000	0.001
vizi-functions	0.043	0.005	0.050
warp1	0.021	0.002	0.023
warp2	0.640	0.010	0.651