Konrad Zych
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SIAMCAT |
| Branch: RELEASE_3_8 |
| Last Commit: 4f0a7ca |
| Last Changed Date: 2019-01-04 13:50:25 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:32 -0400 (Tue, 16 Apr 2019).
| Package 1436/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIAMCAT 1.2.1 Konrad Zych
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SIAMCAT |
| Version: 1.2.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SIAMCAT_1.2.1.tar.gz |
| StartedAt: 2019-04-16 03:03:10 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:06:26 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 196.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIAMCAT.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SIAMCAT_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/SIAMCAT.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.1’
* 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 25.068 0.020 25.162
evaluate.predictions 11.820 0.008 11.851
* 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-3.8-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.
SIAMCAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL SIAMCAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)
SIAMCAT.Rcheck/SIAMCAT-Ex.timings
| name | user | system | elapsed | |
| accessSlot | 0.024 | 0.004 | 0.029 | |
| add.meta.pred | 0.160 | 0.004 | 0.166 | |
| assign-associations | 0.044 | 0.004 | 0.047 | |
| assign-data_split | 0.048 | 0.004 | 0.053 | |
| assign-eval_data | 0.064 | 0.000 | 0.065 | |
| assign-filt_feat | 0.052 | 0.000 | 0.054 | |
| assign-label | 0.040 | 0.000 | 0.041 | |
| assign-meta | 0.048 | 0.000 | 0.048 | |
| assign-model_list | 0.064 | 0.000 | 0.063 | |
| assign-norm_feat | 0.044 | 0.000 | 0.043 | |
| assign-orig_feat | 0.032 | 0.004 | 0.037 | |
| assign-physeq | 0.040 | 0.000 | 0.039 | |
| assign-pred_matrix | 0.036 | 0.000 | 0.033 | |
| assoc_param-methods | 0.012 | 0.000 | 0.014 | |
| associations-methods | 0.024 | 0.000 | 0.028 | |
| check.associations | 0.452 | 0.000 | 0.456 | |
| check.confounders | 0.736 | 0.000 | 0.739 | |
| create.data.split | 0.056 | 0.000 | 0.054 | |
| create.label | 0.004 | 0.000 | 0.005 | |
| data_split-methods | 0.024 | 0.000 | 0.026 | |
| eval_data-methods | 0.024 | 0.008 | 0.035 | |
| evaluate.predictions | 11.820 | 0.008 | 11.851 | |
| feature_type-methods | 0.016 | 0.008 | 0.024 | |
| feature_weights-methods | 0.056 | 0.000 | 0.054 | |
| filt_feat-methods | 0.100 | 0.012 | 0.111 | |
| filt_params-methods | 0.020 | 0.000 | 0.023 | |
| filter.features | 0.064 | 0.000 | 0.067 | |
| filter.label | 0.052 | 0.000 | 0.053 | |
| get.filt_feat.matrix | 0.024 | 0.000 | 0.022 | |
| get.norm_feat.matrix | 0.028 | 0.004 | 0.035 | |
| get.orig_feat.matrix | 0.020 | 0.000 | 0.022 | |
| label-methods | 0.028 | 0.000 | 0.027 | |
| make.predictions | 0.268 | 0.004 | 0.272 | |
| meta-methods | 0.036 | 0.000 | 0.036 | |
| model.evaluation.plot | 0.060 | 0.004 | 0.064 | |
| model.interpretation.plot | 0.108 | 0.000 | 0.110 | |
| model_list-methods | 0.048 | 0.000 | 0.048 | |
| model_type-methods | 0.024 | 0.000 | 0.022 | |
| models-methods | 0.032 | 0.004 | 0.036 | |
| norm_feat-methods | 0.108 | 0.012 | 0.119 | |
| norm_params-methods | 0.024 | 0.000 | 0.025 | |
| normalize.features | 0.604 | 0.000 | 0.612 | |
| orig_feat-methods | 0.236 | 0.076 | 0.313 | |
| physeq-methods | 0.028 | 0.000 | 0.026 | |
| pred_matrix-methods | 0.028 | 0.000 | 0.026 | |
| read.label | 0.008 | 0.008 | 0.028 | |
| read.lefse | 1.096 | 0.028 | 1.149 | |
| select.samples | 0.092 | 0.000 | 0.093 | |
| siamcat | 0.988 | 0.016 | 1.004 | |
| siamcat.to.lefse | 0.052 | 0.000 | 0.051 | |
| siamcat.to.maaslin | 0.064 | 0.000 | 0.064 | |
| summarize.features | 0.66 | 0.00 | 0.66 | |
| train.model | 25.068 | 0.020 | 25.162 | |
| validate.data | 0.072 | 0.000 | 0.072 | |
| weight_matrix-methods | 0.028 | 0.000 | 0.025 | |