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CHECK report for SIAMCAT on merida2

This page was generated on 2018-10-17 09:00:11 -0400 (Wed, 17 Oct 2018).

Package 1362/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 1.0.0
Konrad Zych
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SIAMCAT
Branch: RELEASE_3_7
Last Commit: b5e27eb
Last Changed Date: 2018-04-30 10:35:53 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SIAMCAT
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIAMCAT_1.0.0.tar.gz
StartedAt: 2018-10-17 00:04:19 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:07:45 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 205.6 seconds
RetCode: 0
Status:  OK 
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIAMCAT_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SIAMCAT.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.0’
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
train.model          19.501  0.173  19.767
evaluate.predictions 12.674  0.063  12.833
* 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: OK


Installation output

SIAMCAT.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIAMCAT
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SIAMCAT’ ...
** 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
* DONE (SIAMCAT)

Tests output


Example timings

SIAMCAT.Rcheck/SIAMCAT-Ex.timings

nameusersystemelapsed
accessSlot0.0620.0130.077
add.meta.pred0.2140.0120.226
assign-data_split0.0430.0030.046
assign-eval_data0.0350.0030.038
assign-features0.0620.0040.066
assign-label0.1250.0140.140
assign-meta0.0400.0040.045
assign-model_list0.0460.0040.050
assign-norm_param0.0340.0020.037
assign-orig_feat0.0310.0030.033
assign-physeq0.0330.0010.035
assign-pred_matrix0.0300.0030.033
check.associations2.2970.0482.377
check.confounders1.2350.0221.270
create.data.split0.0590.0030.062
create.label.from.metadata0.0380.0020.040
data_split-methods0.0710.0130.085
eval_data-methods0.0720.0110.084
evaluate.predictions12.674 0.06312.833
features-methods0.4470.1060.558
filter.features0.0670.0030.069
filter.label0.0340.0020.035
get.features.matrix0.0270.0050.032
get.orig_feat.matrix0.0380.0040.042
label-methods0.0390.0040.042
make.predictions3.0500.0123.078
meta-methods0.0500.0090.060
model.evaluation.plot0.0470.0040.053
model.interpretation.plot0.0990.0060.109
model_list-methods0.0380.0040.041
model_type-methods0.0450.0040.049
models-methods0.0360.0020.040
norm_param-methods0.0310.0030.034
normalize.features0.1440.0040.155
orig_feat-methods0.0660.0130.079
physeq-methods0.0380.0030.041
pred_matrix-methods0.0410.0050.045
read.features0.2470.0070.260
read.labels0.0130.0000.014
read.meta0.0040.0000.004
reset.features0.0460.0020.050
select.samples0.0480.0010.049
siamcat0.2310.0120.245
train.model19.501 0.17319.767
validate.data0.0860.0030.088