Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:06:47 -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 palomino3


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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SIAMCAT.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SIAMCAT_2.0.0.tar.gz
StartedAt: 2022-06-24 04:54:06 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:00:12 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 365.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

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


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 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
make.predictions          30.72   0.86   31.58
assign-model_list         29.87   0.73   30.64
model.interpretation.plot 28.25   0.77   29.03
train.model               27.16   0.68   27.84
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck/00check.log'
for details.



Installation output

SIAMCAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library 'F:/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
accessSlot0.030.000.03
add.meta.pred0.040.000.05
assign-associations000
assign-data_split0.020.000.02
assign-eval_data000
assign-filt_feat000
assign-label0.560.000.57
assign-meta0.040.000.03
assign-model_list29.87 0.7330.64
assign-norm_feat0.020.000.01
assign-orig_feat0.010.000.02
assign-physeq0.020.000.02
assign-pred_matrix0.010.000.01
assoc_param-methods0.000.020.02
association.plot0.320.010.33
associations-methods0.030.020.04
check.associations2.340.032.38
check.confounders0.450.030.48
create.data.split0.030.000.03
create.label000
data_split-methods0.000.020.02
eval_data-methods000
evaluate.predictions0.040.000.03
feature_type-methods000
feature_weights-methods0.010.000.02
filt_feat-methods000
filt_params-methods0.000.010.01
filter.features0.020.000.02
filter.label0.010.000.01
get.filt_feat.matrix0.020.000.02
get.norm_feat.matrix0.010.000.01
get.orig_feat.matrix0.020.000.02
label-methods000
make.predictions30.72 0.8631.58
meta-methods0.010.000.01
model.evaluation.plot0.020.000.05
model.interpretation.plot28.25 0.7729.03
model_list-methods000
model_type-methods0.000.010.02
models-methods000
norm_feat-methods0.000.020.01
norm_params-methods000
normalize.features0.020.020.03
orig_feat-methods0.010.000.02
physeq-methods0.020.000.01
pred_matrix-methods0.000.010.02
read.label0.010.000.02
read.lefse0.560.031.15
select.samples0.070.000.06
siamcat0.330.000.33
siamcat.to.lefse0.030.000.03
siamcat.to.maaslin0.030.000.04
summarize.features1.510.061.62
train.model27.16 0.6827.84
validate.data0.020.000.02
volcano.plot0.000.010.02
weight_matrix-methods0.010.000.01