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This page was generated on 2024-07-18 11:39 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
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 1917/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 2.9.0  (landing page)
Jakob Wirbel
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/SIAMCAT
git_branch: devel
git_last_commit: 665aeef
git_last_commit_date: 2024-04-30 11:06:40 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SIAMCAT on nebbiolo2

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: 2.9.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SIAMCAT_2.9.0.tar.gz
StartedAt: 2024-07-18 03:58:48 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 04:09:16 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 628.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SIAMCAT_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.9.0’
* 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 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 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
assign-model_list         28.392  0.715  29.295
make.predictions          28.094  0.339  28.726
train.model               27.583  0.223  28.233
model.interpretation.plot 27.290  0.267  27.837
* 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-3.20-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.


Installation output

SIAMCAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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

SIAMCAT.Rcheck/SIAMCAT-Ex.timings

nameusersystemelapsed
accessSlot0.0130.0000.013
add.meta.pred0.5550.1000.655
assign-associations0.010.000.01
assign-data_split0.0070.0000.007
assign-eval_data0.0090.0000.009
assign-filt_feat0.0070.0040.011
assign-label0.0030.0040.007
assign-meta0.0310.0040.035
assign-model_list28.392 0.71529.295
assign-norm_feat0.0100.0000.011
assign-orig_feat0.0150.0000.015
assign-physeq0.0080.0000.008
assign-pred_matrix0.0060.0030.010
assoc_param-methods0.0040.0040.008
association.plot0.3070.0080.315
associations-methods0.0110.0000.011
check.associations0.0130.0000.013
check.confounders0.5810.0240.605
create.data.split0.0180.0110.029
create.label0.0030.0000.003
data_split-methods0.0070.0000.008
eval_data-methods0.0050.0000.005
evaluate.predictions2.0930.0362.129
feature_type-methods0.0070.0010.007
feature_weights-methods0.0280.0000.028
filt_feat-methods0.0080.0000.008
filt_params-methods0.0060.0000.006
filter.features0.0240.0000.023
filter.label0.0040.0030.008
get.filt_feat.matrix0.0060.0010.006
get.norm_feat.matrix0.0040.0040.008
get.orig_feat.matrix0.0080.0000.008
label-methods0.0070.0000.007
make.predictions28.094 0.33928.726
meta-methods0.0230.0000.023
model.evaluation.plot0.0260.0040.030
model.interpretation.plot27.290 0.26727.837
model_list-methods0.0090.0000.009
model_type-methods0.0090.0000.008
models-methods0.0080.0000.008
norm_feat-methods0.0080.0000.008
norm_params-methods0.0070.0000.007
normalize.features0.0160.0040.021
orig_feat-methods0.0080.0000.008
physeq-methods0.0120.0000.012
pred_matrix-methods0.0080.0000.008
read.label0.0080.0000.011
read.lefse0.8390.0040.861
select.samples0.0700.0000.071
siamcat0.3650.0160.401
siamcat.to.lefse0.0340.0000.034
siamcat.to.maaslin0.0330.0040.037
summarize.features2.2480.0082.333
train.model27.583 0.22328.233
validate.data0.0250.0000.025
volcano.plot0.0160.0000.016
weight_matrix-methods0.0070.0000.007