Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:05:24 -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 nebbiolo1


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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SIAMCAT_2.0.0.tar.gz
StartedAt: 2022-06-23 22:01:48 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 22:06:22 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 274.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SIAMCAT_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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 ... OK
* 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
assign-model_list         24.417  0.201  24.618
make.predictions          23.563  0.224  23.787
model.interpretation.plot 23.462  0.212  23.674
train.model               22.893  0.204  23.097
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.



Installation output

SIAMCAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
accessSlot0.0300.0010.030
add.meta.pred0.0580.0000.058
assign-associations0.0080.0000.008
assign-data_split0.0070.0000.007
assign-eval_data0.0080.0000.008
assign-filt_feat0.0080.0000.008
assign-label0.5750.0040.579
assign-meta0.0220.0030.025
assign-model_list24.417 0.20124.618
assign-norm_feat0.0030.0040.008
assign-orig_feat0.0080.0040.013
assign-physeq0.0040.0040.008
assign-pred_matrix0.0100.0000.009
assoc_param-methods0.0040.0040.008
association.plot0.2120.0040.216
associations-methods0.0060.0040.009
check.associations1.8110.0081.819
check.confounders0.3750.0040.379
create.data.split0.0190.0000.019
create.label0.0020.0000.002
data_split-methods0.0060.0000.005
eval_data-methods0.0020.0040.005
evaluate.predictions0.0190.0000.019
feature_type-methods0.0060.0000.005
feature_weights-methods0.0020.0040.005
filt_feat-methods0.0060.0000.005
filt_params-methods0.0010.0040.005
filter.features0.0130.0000.013
filter.label0.0060.0000.006
get.filt_feat.matrix0.0050.0000.006
get.norm_feat.matrix0.0050.0000.006
get.orig_feat.matrix0.0190.0000.020
label-methods0.0060.0000.006
make.predictions23.563 0.22423.787
meta-methods0.0180.0040.023
model.evaluation.plot0.0260.0000.026
model.interpretation.plot23.462 0.21223.674
model_list-methods0.0060.0000.006
model_type-methods0.0060.0000.005
models-methods0.0020.0040.006
norm_feat-methods0.0060.0000.005
norm_params-methods0.0060.0000.006
normalize.features0.0100.0040.014
orig_feat-methods0.0060.0000.006
physeq-methods0.0070.0040.009
pred_matrix-methods0.0060.0000.007
read.label0.0090.0000.010
read.lefse0.5060.0160.523
select.samples0.0460.0040.051
siamcat0.2980.0120.310
siamcat.to.lefse0.0220.0000.023
siamcat.to.maaslin0.0200.0030.024
summarize.features1.3780.0081.386
train.model22.893 0.20423.097
validate.data0.0180.0000.019
volcano.plot0.0120.0000.012
weight_matrix-methods0.0020.0030.006