Jakob Wirbel
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/SIAMCAT |
| git_branch: RELEASE_3_13 |
| git_last_commit: fb65d54 |
| git_last_commit_date: 2021-05-19 12:35:49 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:53 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the SIAMCAT package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIAMCAT.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1754/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIAMCAT 1.12.0 (landing page) Jakob Wirbel
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SIAMCAT |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SIAMCAT_1.12.0.tar.gz |
| StartedAt: 2021-10-14 11:36:50 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:39:38 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 168.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIAMCAT.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SIAMCAT_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 LazyData ... OK
* 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 18.568 0.54 19.113
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.
SIAMCAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SIAMCAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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)
SIAMCAT.Rcheck/SIAMCAT-Ex.timings
| name | user | system | elapsed | |
| accessSlot | 0.044 | 0.004 | 0.048 | |
| add.meta.pred | 0.059 | 0.008 | 0.066 | |
| assign-associations | 0.533 | 0.000 | 0.534 | |
| assign-data_split | 0.016 | 0.000 | 0.016 | |
| assign-eval_data | 0.016 | 0.000 | 0.016 | |
| assign-filt_feat | 0.017 | 0.000 | 0.016 | |
| assign-label | 0.013 | 0.003 | 0.017 | |
| assign-meta | 0.041 | 0.000 | 0.040 | |
| assign-model_list | 0.015 | 0.000 | 0.015 | |
| assign-norm_feat | 0.015 | 0.000 | 0.016 | |
| assign-orig_feat | 0.019 | 0.000 | 0.019 | |
| assign-physeq | 0.015 | 0.000 | 0.015 | |
| assign-pred_matrix | 0.015 | 0.000 | 0.015 | |
| assoc_param-methods | 0.02 | 0.00 | 0.02 | |
| associations-methods | 0.018 | 0.001 | 0.018 | |
| check.associations | 0.217 | 0.000 | 0.217 | |
| check.confounders | 0.387 | 0.003 | 0.390 | |
| create.data.split | 0.030 | 0.000 | 0.029 | |
| create.label | 0.004 | 0.000 | 0.003 | |
| data_split-methods | 0.012 | 0.004 | 0.015 | |
| eval_data-methods | 0.023 | 0.000 | 0.023 | |
| evaluate.predictions | 1.593 | 0.004 | 1.598 | |
| feature_type-methods | 0.012 | 0.004 | 0.016 | |
| feature_weights-methods | 0.017 | 0.003 | 0.021 | |
| filt_feat-methods | 0.026 | 0.000 | 0.026 | |
| filt_params-methods | 0.011 | 0.004 | 0.015 | |
| filter.features | 0.016 | 0.004 | 0.021 | |
| filter.label | 0.018 | 0.000 | 0.018 | |
| get.filt_feat.matrix | 0.022 | 0.004 | 0.026 | |
| get.norm_feat.matrix | 0.011 | 0.004 | 0.015 | |
| get.orig_feat.matrix | 0.011 | 0.004 | 0.015 | |
| label-methods | 0.015 | 0.000 | 0.014 | |
| make.predictions | 0.155 | 0.004 | 0.160 | |
| meta-methods | 0.025 | 0.004 | 0.030 | |
| model.evaluation.plot | 0.041 | 0.000 | 0.041 | |
| model.interpretation.plot | 0.059 | 0.004 | 0.063 | |
| model_list-methods | 0.015 | 0.000 | 0.014 | |
| model_type-methods | 0.039 | 0.000 | 0.039 | |
| models-methods | 0.018 | 0.000 | 0.018 | |
| norm_feat-methods | 0.016 | 0.000 | 0.016 | |
| norm_params-methods | 0.017 | 0.000 | 0.017 | |
| normalize.features | 0.036 | 0.004 | 0.040 | |
| orig_feat-methods | 0.016 | 0.000 | 0.016 | |
| physeq-methods | 0.019 | 0.000 | 0.020 | |
| pred_matrix-methods | 0.033 | 0.000 | 0.033 | |
| read.label | 0.01 | 0.00 | 0.01 | |
| read.lefse | 0.543 | 0.028 | 0.574 | |
| select.samples | 0.597 | 0.004 | 0.602 | |
| siamcat | 0.238 | 0.000 | 0.237 | |
| siamcat.to.lefse | 0.034 | 0.000 | 0.033 | |
| siamcat.to.maaslin | 0.561 | 0.015 | 0.577 | |
| summarize.features | 1.130 | 0.048 | 1.179 | |
| train.model | 18.568 | 0.540 | 19.113 | |
| validate.data | 0.027 | 0.012 | 0.040 | |
| weight_matrix-methods | 0.017 | 0.000 | 0.016 | |