Multiple platform build/check report for BioC 3.21 - CHECK results for matter on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4480
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4444
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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings matter_2.9.1.tar.gz

StartedAt: 2025-02-05 23:50:57 -0500 (Wed, 05 Feb 2025)

EndedAt: 2025-02-05 23:54:38 -0500 (Wed, 05 Feb 2025)

EllapsedTime: 221.3 seconds

RetCode: 0

Status: OK

CheckDir: matter.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings matter_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/matter.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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: ‘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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/matter.Rcheck/00check.log’
for details.

Installation output

matter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL matter
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘matter’ ...
** this is package ‘matter’ version ‘2.9.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c altrep.cpp -o altrep.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c init.cpp -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c matterExports.cpp -o matterExports.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o matter.so altrep.o init.o matterExports.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-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) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 76.813   2.733  94.973

Example timings

matter.Rcheck/matter-Ex.timings

name	user	system	elapsed
RNGStreams	1.059	0.005	1.065
SnowfastParam-class	0.204	0.019	2.603
approx1	0.002	0.001	0.003
approx2	0.004	0.001	0.005
avg	0.002	0.000	0.002
binpeaks	0.004	0.002	0.006
binvec	0.001	0.000	0.001
bsearch	0.001	0.000	0.001
checksum	0.023	0.005	0.028
chunkApply	0.190	0.021	0.211
chunked-class	0.006	0.001	0.007
colscale	0.159	0.002	0.161
colsweep	0.021	0.001	0.022
convolve_at	0.078	0.003	0.081
coscore	0.035	0.008	0.042
cpal	0.003	0.000	0.003
cv_do	0.155	0.002	0.157
deferred-ops	0.204	0.012	0.216
downsample	0.034	0.001	0.035
drle-class	0.001	0.001	0.002
enhance	0.020	0.003	0.023
estbase	0.012	0.001	0.013
estdim	0.004	0.000	0.004
estnoise	0.034	0.004	0.038
estres	0.001	0.000	0.001
fastmap	0.111	0.002	0.114
fetch	0.090	0.005	0.096
filt1	0.032	0.000	0.033
filt2	0.023	0.000	0.023
filtn	0.003	0.001	0.004
findpeaks	0.027	0.001	0.028
findpeaks_cwt	0.123	0.006	0.128
findpeaks_knn	0.003	0.000	0.003
iQuote	0.001	0.000	0.000
inpoly	0.003	0.001	0.004
isofun	0.022	0.001	0.023
knnsearch	0.002	0.000	0.001
matter-class	0.022	0.002	0.023
matter_arr-class	0.026	0.000	0.026
matter_fct-class	0.016	0.001	0.016
matter_list-class	0.009	0.001	0.009
matter_str-class	0.019	0.001	0.019
mem	0.389	0.004	0.392
mi_learn	0.514	0.002	0.516
nnmf	0.039	0.001	0.039
nscentroids	0.086	0.002	0.087
peakwidths	0.001	0.001	0.001
pinv	0.001	0.002	0.002
plot_signal	0.447	0.009	0.456
pls	0.037	0.000	0.037
prcomp	0.088	0.000	0.087
predscore	0.001	0.000	0.001
rescale	0.001	0.000	0.000
rocscore	0.002	0.001	0.003
rollvec	0.002	0.000	0.001
rowDists	0.079	0.001	0.079
rowStats	0.095	0.004	0.099
seq_rel	0.001	0.001	0.002
sgmix	2.197	0.013	2.210
shingles	0.001	0.003	0.003
simple_logger-class	0.004	0.002	0.005
simspec	0.038	0.001	0.038
sparse_arr-class	0.007	0.001	0.008
stream_stat	0.005	0.001	0.006
struct	0.005	0.001	0.006
summary-stats	0.304	0.004	0.308
to_raster	0.002	0.002	0.004
trans2d	0.039	0.001	0.040
uuid	0.001	0.000	0.002
vizi-functions	0.051	0.003	0.055
warp1	0.030	0.004	0.034
warp2	0.834	0.002	0.836