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CHECK report for SIAMCAT on celaya2

This page was generated on 2019-04-09 13:20:31 -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: /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_1.3.1.tar.gz
StartedAt: 2019-04-09 05:29:16 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:34:21 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 304.7 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_1.3.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.1’
* 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          30.168  0.167  31.352
evaluate.predictions 20.514  0.160  21.194
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.



Installation output

SIAMCAT.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIAMCAT
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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
accessSlot0.0540.0190.073
add.meta.pred0.3160.0100.327
assign-associations0.0610.0090.070
assign-data_split0.0690.0110.080
assign-eval_data0.0360.0030.039
assign-filt_feat0.0560.0040.073
assign-label0.0520.0030.087
assign-meta0.0970.0050.116
assign-model_list0.0550.0020.057
assign-norm_feat0.0520.0050.057
assign-orig_feat0.0530.0060.058
assign-physeq0.0640.0020.066
assign-pred_matrix0.0520.0030.055
assoc_param-methods0.0220.0040.026
associations-methods0.0500.0070.057
check.associations0.7540.0670.823
check.confounders1.4780.0791.562
create.data.split0.1030.0070.110
create.label0.0110.0020.013
data_split-methods0.0590.0250.082
eval_data-methods0.0560.0400.096
evaluate.predictions20.514 0.16021.194
feature_type-methods0.0220.0020.024
feature_weights-methods0.0720.0070.080
filt_feat-methods0.2010.0810.283
filt_params-methods0.0220.0030.026
filter.features0.0900.0050.098
filter.label0.0550.0020.058
get.filt_feat.matrix0.0200.0010.023
get.norm_feat.matrix0.0430.0020.045
get.orig_feat.matrix0.0190.0030.021
label-methods0.0640.0190.087
make.predictions0.3230.0070.340
meta-methods0.0460.0120.058
model.evaluation.plot0.0640.0040.071
model.interpretation.plot0.1260.0070.136
model_list-methods0.0630.0040.068
model_type-methods0.0200.0010.022
models-methods0.0310.0030.034
norm_feat-methods0.2220.0750.308
norm_params-methods0.0210.0020.023
normalize.features0.1300.0030.193
orig_feat-methods0.5920.2370.838
physeq-methods0.0200.0020.022
pred_matrix-methods0.0190.0050.023
read.label0.0370.0010.038
read.lefse2.0050.0552.067
select.samples0.1720.0030.174
siamcat1.0040.0351.040
siamcat.to.lefse0.0490.0030.062
siamcat.to.maaslin0.0510.0030.088
summarize.features0.8610.0360.899
train.model30.168 0.16731.352
validate.data0.0820.0020.090
weight_matrix-methods0.0330.0070.041