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This page was generated on 2022-06-24 12:08:10 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 SIAMCAT on merida1


To the developers/maintainers of the SIAMCAT package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1832/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 2.0.0  (landing page)
Jakob Wirbel
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/SIAMCAT
git_branch: RELEASE_3_15
git_last_commit: 2f7b943
git_last_commit_date: 2022-04-26 11:49:17 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: SIAMCAT
Version: 2.0.0
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_2.0.0.tar.gz
StartedAt: 2022-06-24 08:53:54 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 09:05:23 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 688.8 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_2.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.0.0’
* 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 48.424  0.482  61.317
assign-model_list         47.967  0.550  61.174
make.predictions          48.018  0.458  60.275
train.model               47.743  0.527  60.100
check.associations         4.320  0.015   5.551
* 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
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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
accessSlot0.0150.0040.020
add.meta.pred0.1120.0020.149
assign-associations0.0130.0020.021
assign-data_split0.0140.0030.019
assign-eval_data0.0140.0020.017
assign-filt_feat0.0130.0010.022
assign-label0.6520.0030.822
assign-meta0.0520.0020.066
assign-model_list47.967 0.55061.174
assign-norm_feat0.0140.0010.018
assign-orig_feat0.0220.0010.028
assign-physeq0.0130.0020.021
assign-pred_matrix0.0140.0020.020
assoc_param-methods0.0100.0030.016
association.plot0.3950.0140.511
associations-methods0.0170.0020.024
check.associations4.3200.0155.551
check.confounders0.8350.0241.096
create.data.split0.0470.0020.057
create.label0.0040.0010.005
data_split-methods0.0100.0010.016
eval_data-methods0.0110.0010.014
evaluate.predictions0.0490.0030.061
feature_type-methods0.0100.0020.019
feature_weights-methods0.0110.0020.014
filt_feat-methods0.0100.0010.013
filt_params-methods0.0100.0010.017
filter.features0.0280.0030.038
filter.label0.0130.0010.018
get.filt_feat.matrix0.0110.0020.019
get.norm_feat.matrix0.0110.0030.015
get.orig_feat.matrix0.0330.0030.045
label-methods0.0120.0020.017
make.predictions48.018 0.45860.275
meta-methods0.0370.0020.056
model.evaluation.plot0.0420.0070.069
model.interpretation.plot48.424 0.48261.317
model_list-methods0.0110.0020.017
model_type-methods0.0110.0030.016
models-methods0.0110.0020.013
norm_feat-methods0.0100.0030.015
norm_params-methods0.0100.0020.013
normalize.features0.0270.0020.036
orig_feat-methods0.0110.0020.015
physeq-methods0.0160.0020.020
pred_matrix-methods0.0110.0020.014
read.label0.0180.0000.020
read.lefse1.3930.0161.632
select.samples0.1170.0020.141
siamcat0.4640.0140.564
siamcat.to.lefse0.0380.0030.051
siamcat.to.maaslin0.0400.0020.052
summarize.features2.7810.1493.620
train.model47.743 0.52760.100
validate.data0.0350.0020.053
volcano.plot0.0210.0020.032
weight_matrix-methods0.0100.0010.014