Konrad Zych
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/SIAMCAT |
| Branch: RELEASE_3_11 |
| Last Commit: e46a68a |
| Last Changed Date: 2020-06-30 04:46:36 -0400 (Tue, 30 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:45 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE SIAMCAT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1647/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIAMCAT 1.8.1 Konrad Zych
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: SIAMCAT |
| Version: 1.8.1 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SIAMCAT_1.8.1.tar.gz |
| StartedAt: 2020-10-17 05:28:54 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:32:20 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 206.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIAMCAT.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SIAMCAT_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.8.1’
* 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 (user + system) or elapsed time > 5s
user system elapsed
train.model 24.485 0.019 24.533
evaluate.predictions 8.963 0.052 9.015
* 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-3.11-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.
SIAMCAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL SIAMCAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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 ** 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)
SIAMCAT.Rcheck/SIAMCAT-Ex.timings
| name | user | system | elapsed | |
| accessSlot | 0.022 | 0.004 | 0.026 | |
| add.meta.pred | 0.067 | 0.000 | 0.068 | |
| assign-associations | 0.028 | 0.000 | 0.027 | |
| assign-data_split | 0.017 | 0.000 | 0.016 | |
| assign-eval_data | 0.017 | 0.000 | 0.017 | |
| assign-filt_feat | 0.023 | 0.000 | 0.023 | |
| assign-label | 0.016 | 0.000 | 0.015 | |
| assign-meta | 0.036 | 0.000 | 0.037 | |
| assign-model_list | 0.517 | 0.000 | 0.518 | |
| assign-norm_feat | 0.026 | 0.000 | 0.026 | |
| assign-orig_feat | 0.035 | 0.000 | 0.035 | |
| assign-physeq | 0.027 | 0.000 | 0.027 | |
| assign-pred_matrix | 0.027 | 0.000 | 0.027 | |
| assoc_param-methods | 0.025 | 0.000 | 0.024 | |
| associations-methods | 0.036 | 0.004 | 0.040 | |
| check.associations | 0.361 | 0.008 | 0.369 | |
| check.confounders | 0.673 | 0.008 | 0.681 | |
| create.data.split | 0.049 | 0.000 | 0.050 | |
| create.label | 0.006 | 0.000 | 0.006 | |
| data_split-methods | 0.023 | 0.000 | 0.022 | |
| eval_data-methods | 0.022 | 0.000 | 0.023 | |
| evaluate.predictions | 8.963 | 0.052 | 9.015 | |
| feature_type-methods | 0.011 | 0.004 | 0.015 | |
| feature_weights-methods | 0.018 | 0.004 | 0.021 | |
| filt_feat-methods | 0.012 | 0.004 | 0.016 | |
| filt_params-methods | 0.024 | 0.000 | 0.025 | |
| filter.features | 0.020 | 0.000 | 0.019 | |
| filter.label | 0.016 | 0.000 | 0.016 | |
| get.filt_feat.matrix | 0.015 | 0.000 | 0.014 | |
| get.norm_feat.matrix | 0.013 | 0.004 | 0.016 | |
| get.orig_feat.matrix | 0.023 | 0.000 | 0.023 | |
| label-methods | 0.014 | 0.000 | 0.015 | |
| make.predictions | 0.155 | 0.004 | 0.157 | |
| meta-methods | 0.045 | 0.000 | 0.045 | |
| model.evaluation.plot | 0.024 | 0.003 | 0.029 | |
| model.interpretation.plot | 0.071 | 0.000 | 0.072 | |
| model_list-methods | 0.014 | 0.000 | 0.015 | |
| model_type-methods | 0.025 | 0.000 | 0.024 | |
| models-methods | 0.016 | 0.000 | 0.016 | |
| norm_feat-methods | 0.015 | 0.000 | 0.015 | |
| norm_params-methods | 0.015 | 0.000 | 0.014 | |
| normalize.features | 0.062 | 0.000 | 0.062 | |
| orig_feat-methods | 0.012 | 0.004 | 0.015 | |
| physeq-methods | 0.019 | 0.000 | 0.019 | |
| pred_matrix-methods | 0.015 | 0.000 | 0.015 | |
| read.label | 0.008 | 0.000 | 0.014 | |
| read.lefse | 1.069 | 0.003 | 1.077 | |
| select.samples | 0.12 | 0.00 | 0.12 | |
| siamcat | 0.354 | 0.003 | 0.358 | |
| siamcat.to.lefse | 0.036 | 0.000 | 0.036 | |
| siamcat.to.maaslin | 0.059 | 0.000 | 0.059 | |
| summarize.features | 1.675 | 0.032 | 1.707 | |
| train.model | 24.485 | 0.019 | 24.533 | |
| validate.data | 0.049 | 0.000 | 0.050 | |
| weight_matrix-methods | 0.028 | 0.000 | 0.027 | |