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This page was generated on 2024-03-04 11:39:56 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R 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

Package 1927/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 2.7.2  (landing page)
Jakob Wirbel
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/SIAMCAT
git_branch: devel
git_last_commit: 6fcb862
git_last_commit_date: 2024-01-29 19:36:00 -0500 (Mon, 29 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for SIAMCAT on merida1


To the developers/maintainers of the SIAMCAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIAMCAT.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: SIAMCAT
Version: 2.7.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIAMCAT_2.7.2.tar.gz
StartedAt: 2024-03-02 10:39:14 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 10:49:39 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 625.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIAMCAT_2.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SIAMCAT.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 ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.7.2’
* 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 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
model.interpretation.plot 41.921  0.866  47.470
train.model               41.878  0.799  49.625
assign-model_list         41.529  0.876  49.548
make.predictions          40.734  0.622  47.161
evaluate.predictions       4.179  0.142   5.084
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.



Installation output

SIAMCAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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

SIAMCAT.Rcheck/SIAMCAT-Ex.timings

nameusersystemelapsed
accessSlot0.0140.0100.026
add.meta.pred0.0510.0040.062
assign-associations0.0120.0030.023
assign-data_split0.0130.0030.018
assign-eval_data0.0120.0030.016
assign-filt_feat0.5150.0070.607
assign-label0.0120.0020.018
assign-meta0.0540.0040.070
assign-model_list41.529 0.87649.548
assign-norm_feat0.0120.0030.017
assign-orig_feat0.0390.0030.049
assign-physeq0.0130.0030.018
assign-pred_matrix0.0120.0030.018
assoc_param-methods0.0090.0030.012
association.plot0.4080.0280.511
associations-methods0.0150.0040.022
check.associations0.0180.0040.023
check.confounders0.9600.0491.168
create.data.split0.0480.0030.057
create.label0.0040.0030.007
data_split-methods0.0080.0030.013
eval_data-methods0.0090.0030.015
evaluate.predictions4.1790.1425.084
feature_type-methods0.0080.0020.013
feature_weights-methods0.0090.0030.014
filt_feat-methods0.0090.0020.012
filt_params-methods0.0080.0030.014
filter.features0.0260.0030.039
filter.label0.0120.0030.015
get.filt_feat.matrix0.0090.0030.016
get.norm_feat.matrix0.0360.0060.052
get.orig_feat.matrix0.0090.0030.016
label-methods0.0100.0030.014
make.predictions40.734 0.62247.161
meta-methods0.0350.0050.051
model.evaluation.plot0.0440.0171.676
model.interpretation.plot41.921 0.86647.470
model_list-methods0.0090.0030.014
model_type-methods0.0080.0030.013
models-methods0.0090.0030.012
norm_feat-methods0.0080.0030.013
norm_params-methods0.0090.0020.012
normalize.features0.0260.0040.041
orig_feat-methods0.0090.0020.011
physeq-methods0.0150.0020.018
pred_matrix-methods0.0100.0030.015
read.label0.0190.0020.027
read.lefse1.3940.0381.936
select.samples0.1280.0090.148
siamcat0.4610.0300.585
siamcat.to.lefse0.0360.0050.051
siamcat.to.maaslin0.0390.0040.043
summarize.features2.5800.1833.129
train.model41.878 0.79949.625
validate.data0.0370.0030.056
volcano.plot0.0200.0050.032
weight_matrix-methods0.0090.0020.012