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CHECK report for SIAMCAT on malbec2

This page was generated on 2019-04-09 11:50:58 -0400 (Tue, 09 Apr 2019).

Package 1480/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 1.3.1
Konrad Zych
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SIAMCAT
Branch: master
Last Commit: da10be5
Last Changed Date: 2019-01-04 13:50:16 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: SIAMCAT
Version: 1.3.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SIAMCAT_1.3.1.tar.gz
StartedAt: 2019-04-09 03:38:11 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:41:36 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 205.6 seconds
RetCode: 0
Status:  OK 
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SIAMCAT_1.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.1’
* 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 ... NOTE
  Note: found 10 marked UTF-8 strings
* 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          22.281  0.028  22.416
evaluate.predictions 13.785  0.031  13.836
* 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-3.9-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.



Installation output

SIAMCAT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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
accessSlot0.0460.0000.052
add.meta.pred0.2480.0040.252
assign-associations0.5740.0000.575
assign-data_split0.0450.0000.045
assign-eval_data0.0430.0040.047
assign-filt_feat0.0360.0120.047
assign-label0.0280.0120.040
assign-meta0.0610.0000.061
assign-model_list0.0380.0000.038
assign-norm_feat0.0390.0000.039
assign-orig_feat0.0410.0000.041
assign-physeq0.0490.0000.049
assign-pred_matrix0.0450.0000.045
assoc_param-methods0.0210.0000.022
associations-methods0.0310.0000.031
check.associations0.9670.0000.973
check.confounders1.0340.0281.074
create.data.split0.0640.0160.080
create.label0.0090.0000.009
data_split-methods0.0380.0040.045
eval_data-methods0.0300.0080.038
evaluate.predictions13.785 0.03113.836
feature_type-methods0.0210.0000.021
feature_weights-methods0.0290.0040.034
filt_feat-methods0.0890.0040.093
filt_params-methods0.0160.0000.015
filter.features0.0440.0000.044
filter.label0.0290.0000.029
get.filt_feat.matrix0.0140.0000.014
get.norm_feat.matrix0.0140.0000.014
get.orig_feat.matrix0.0150.0000.015
label-methods0.020.000.02
make.predictions0.2540.0040.257
meta-methods0.0300.0040.034
model.evaluation.plot0.0330.0000.034
model.interpretation.plot0.1060.0000.105
model_list-methods0.0320.0000.033
model_type-methods0.0220.0000.022
models-methods0.0450.0000.044
norm_feat-methods0.0900.0160.107
norm_params-methods0.0230.0000.022
normalize.features0.0870.0040.091
orig_feat-methods0.1870.0200.207
physeq-methods0.0170.0000.016
pred_matrix-methods0.0230.0040.026
read.label0.0100.0000.015
read.lefse0.8240.0120.849
select.samples0.2110.0000.211
siamcat0.480.000.48
siamcat.to.lefse0.0870.0000.087
siamcat.to.maaslin0.0560.0000.056
summarize.features0.6410.0120.662
train.model22.281 0.02822.416
validate.data0.0750.0000.092
weight_matrix-methods0.0330.0000.033