Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1909/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 2.9.0  (landing page)
Jakob Wirbel
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SIAMCAT on palomino4

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SIAMCAT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SIAMCAT_2.9.0.tar.gz
StartedAt: 2024-06-10 09:43:11 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 09:53:28 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 616.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SIAMCAT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SIAMCAT_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SIAMCAT.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SIAMCAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIAMCAT' version '2.9.0'
* 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 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 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
make.predictions          22.33   1.06   23.47
model.interpretation.plot 22.18   0.81   23.05
train.model               21.58   0.98   22.69
assign-model_list         21.56   0.94   22.56
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/SIAMCAT.Rcheck/00check.log'
for details.


Installation output

SIAMCAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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
accessSlot0.020.000.01
add.meta.pred0.030.020.05
assign-associations0.110.000.11
assign-data_split0.010.000.02
assign-eval_data0.020.000.01
assign-filt_feat0.010.000.02
assign-label000
assign-meta0.030.000.03
assign-model_list21.56 0.9422.56
assign-norm_feat0.000.020.01
assign-orig_feat0.020.000.02
assign-physeq0.010.000.02
assign-pred_matrix0.000.010.01
assoc_param-methods000
association.plot0.250.030.28
associations-methods0.020.000.02
check.associations0.030.000.03
check.confounders0.590.070.66
create.data.split0.020.010.03
create.label000
data_split-methods0.000.020.01
eval_data-methods000
evaluate.predictions1.700.081.78
feature_type-methods0.070.010.08
feature_weights-methods000
filt_feat-methods000
filt_params-methods0.020.000.02
filter.features0.010.000.01
filter.label0.020.000.02
get.filt_feat.matrix000
get.norm_feat.matrix000
get.orig_feat.matrix0.010.000.02
label-methods0.000.020.01
make.predictions22.33 1.0623.47
meta-methods0.020.020.03
model.evaluation.plot0.040.010.08
model.interpretation.plot22.18 0.8123.05
model_list-methods000
model_type-methods0.010.000.01
models-methods0.020.000.02
norm_feat-methods000
norm_params-methods0.010.000.01
normalize.features0.020.000.02
orig_feat-methods0.010.000.02
physeq-methods000
pred_matrix-methods0.000.020.01
read.label0.000.020.02
read.lefse0.790.070.87
select.samples0.070.000.08
siamcat0.270.020.28
siamcat.to.lefse0.030.000.03
siamcat.to.maaslin0.030.000.03
summarize.features1.340.251.59
train.model21.58 0.9822.69
validate.data0.010.020.03
volcano.plot0.020.000.02
weight_matrix-methods0.020.000.01