Multiple platform build/check report for BioC 3.19 - CHECK results for matter on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"	4676
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences"	4414
merida1	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"	4441
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences"	4417
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*

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### Running command:
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###   /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_2.5.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/matter.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matter’ version ‘2.5.4’
* 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 ... WARNING
Found the following significant warnings:
  altrep.cpp:112:65: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  altrep.cpp:242:67: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/matter.Rcheck/00install.out’ for details.
* 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 R 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’
 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/matter.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL matter
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* 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/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c altrep.cpp -o altrep.o
altrep.cpp:112:65: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
        Rprintf("matter array (mode=%d, len=%d, mem=%d)\n", xm.type(), xm.length(), mem);
                                            ~~                         ^~~~~~~~~~~
                                            %td
altrep.cpp:242:67: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
        Rprintf("matter strings (mode=%d, len=%d, mem=%d)\n", xm.type(), xm.length(), mem);
                                              ~~                         ^~~~~~~~~~~
                                              %td
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.cpp -o init.o
In file included from init.cpp:3:
In file included from ./matterExports.h:13:
./signal2.h:153:24: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
        index_t ii, jj, prev, lo, hi;
                              ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c matterExports.cpp -o matterExports.o
In file included from matterExports.cpp:2:
In file included from ./matterExports.h:13:
./signal2.h:153:24: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
        index_t ii, jj, prev, lo, hi;
                              ^
1 warning generated.
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


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(testthat)
> library(matter)
Loading required package: BiocParallel
Loading required package: Matrix
> 
> test_check("matter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1349 ]
> 
> proc.time()
   user  system elapsed 
 72.490   3.064  89.786

Example timings

name	user	system	elapsed
approx1	0.005	0.002	0.012
approx2	0.011	0.004	0.022
asearch	0.001	0.001	0.003
biglm	0.196	0.011	0.262
binpeaks	0.009	0.001	0.018
binvec	0.001	0.000	0.004
bsearch	0.002	0.001	0.004
checksum	0.036	0.003	0.049
chunkApply	1.269	0.030	1.566
colscale	0.164	0.006	0.204
colsweep	0.028	0.002	0.037
convolve_at	0.256	0.018	0.328
cpal	0.005	0.000	0.006
deferred-ops	0.095	0.007	0.115
downsample	0.064	0.004	0.082
drle-class	0.003	0.001	0.003
enhance	0.040	0.005	0.051
estbase	0.017	0.003	0.024
estdim	0.005	0.001	0.008
estnoise	0.107	0.007	0.142
estres	0.000	0.000	0.001
fastmap	0.413	0.040	0.533
filt1	0.033	0.004	0.049
filt2	0.040	0.004	0.053
findpeaks	0.06	0.01	0.08
findpeaks_cwt	0.203	0.018	0.267
image	0.232	0.018	0.302
inpoly	0.007	0.002	0.011
knnsearch	0.002	0.000	0.004
matter-class	0.054	0.005	0.070
matter_arr-class	0.049	0.003	0.061
matter_fct-class	0.037	0.002	0.047
matter_list-class	0.018	0.003	0.027
matter_str-class	0.029	0.004	0.041
memtime	0.495	0.006	0.592
nnmf	0.024	0.001	0.029
peakwidths	0.002	0.001	0.002
pls	0.058	0.001	0.074
prcomp	0.119	0.018	0.163
rollvec	0.001	0.000	0.002
rowDists	0.087	0.004	0.109
rowStats	0.234	0.010	0.288
simspec	0.054	0.005	0.071
sparse_arr-class	0.013	0.003	0.021
stream-stats	0.012	0.002	0.018
struct	0.012	0.002	0.016
summary-stats	0.293	0.021	0.366
to_raster	0.006	0.004	0.012
trans2d	0.066	0.005	0.089
uuid	0.001	0.001	0.003
vizi	0.132	0.020	0.187
warp1	0.063	0.006	0.083
warp2	1.467	0.035	1.762

CHECK results for matter on merida1

Summary

Command output

Installation output

Tests output

Example timings