Multiple platform build/check report for BioC 3.18 - CHECK results for SIAMCAT on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.2 LTS)	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4729
palomino4	Windows Server 2022 Datacenter	x64	4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"	4463
lconway	macOS 12.6.5 Monterey	x86_64	4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts"	4478
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4464
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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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings SIAMCAT_2.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.6.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SIAMCAT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    help      1.9Mb
* 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
train.model               30.823  0.328  31.225
assign-model_list         30.475  0.550  31.098
make.predictions          29.708  0.459  30.229
model.interpretation.plot 29.739  0.264  30.066
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘SIAMCAT’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SIAMCAT)

Tests output

Example timings

name	user	system	elapsed
accessSlot	0.011	0.000	0.011
add.meta.pred	0.038	0.000	0.038
assign-associations	0.009	0.000	0.009
assign-data_split	0.009	0.000	0.008
assign-eval_data	0.001	0.008	0.009
assign-filt_feat	0.009	0.000	0.009
assign-label	0.027	0.004	0.031
assign-meta	0.033	0.004	0.037
assign-model_list	30.475	0.550	31.098
assign-norm_feat	0.009	0.000	0.009
assign-orig_feat	0.010	0.004	0.015
assign-physeq	0.009	0.000	0.009
assign-pred_matrix	0.009	0.000	0.008
assoc_param-methods	0.003	0.004	0.007
association.plot	0.262	0.008	0.271
associations-methods	0.008	0.003	0.011
check.associations	0.009	0.004	0.012
check.confounders	0.580	0.004	0.586
create.data.split	0.029	0.000	0.028
create.label	0.002	0.001	0.003
data_split-methods	0.004	0.003	0.007
eval_data-methods	0.007	0.000	0.007
evaluate.predictions	2.298	0.012	2.314
feature_type-methods	0.002	0.004	0.007
feature_weights-methods	0.007	0.000	0.007
filt_feat-methods	0.007	0.000	0.006
filt_params-methods	0.025	0.000	0.026
filter.features	0.021	0.000	0.021
filter.label	0.009	0.000	0.010
get.filt_feat.matrix	0.007	0.000	0.007
get.norm_feat.matrix	0.007	0.000	0.007
get.orig_feat.matrix	0.007	0.000	0.007
label-methods	0.008	0.000	0.007
make.predictions	29.708	0.459	30.229
meta-methods	0.020	0.004	0.024
model.evaluation.plot	0.026	0.004	0.029
model.interpretation.plot	29.739	0.264	30.066
model_list-methods	0.008	0.000	0.008
model_type-methods	0.008	0.000	0.007
models-methods	0.007	0.000	0.007
norm_feat-methods	0.008	0.000	0.008
norm_params-methods	0.003	0.004	0.007
normalize.features	0.019	0.000	0.018
orig_feat-methods	0.008	0.000	0.008
physeq-methods	0.007	0.004	0.012
pred_matrix-methods	0.007	0.000	0.007
read.label	0.006	0.004	0.011
read.lefse	0.950	0.020	0.973
select.samples	0.082	0.000	0.083
siamcat	0.344	0.004	0.350
siamcat.to.lefse	0.021	0.000	0.022
siamcat.to.maaslin	0.023	0.000	0.023
summarize.features	2.641	0.031	2.682
train.model	30.823	0.328	31.225
validate.data	0.049	0.000	0.049
volcano.plot	0.014	0.000	0.015
weight_matrix-methods	0.007	0.000	0.007

CHECK results for SIAMCAT on kunpeng2

Summary

Command output

Installation output

Tests output

Example timings