| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:29 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1849/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIAMCAT 2.3.0 (landing page) Jakob Wirbel
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: SIAMCAT |
| Version: 2.3.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SIAMCAT_2.3.0.tar.gz |
| StartedAt: 2023-02-07 15:39:19 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 16:06:25 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 1626.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SIAMCAT.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SIAMCAT_2.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.3.0’
* 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 ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
extdata 2.1Mb
help 1.9Mb
* 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 ... OK
* 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
make.predictions 28.991 0.216 29.224
assign-model_list 28.822 0.256 29.104
model.interpretation.plot 27.707 0.563 29.496
train.model 27.904 0.164 28.083
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘SIAMCAT_confounder.Rmd’ using ‘ASCII’... OK
‘SIAMCAT_holdout.Rmd’ using ‘ASCII’... OK
‘SIAMCAT_meta.Rmd’ using ‘ASCII’... OK
‘SIAMCAT_ml_pitfalls.Rmd’ using ‘ASCII’... OK
‘SIAMCAT_read-in.Rmd’ using ‘ASCII’... OK
‘SIAMCAT_vignette.Rmd’ using ‘ASCII’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘SIAMCAT_confounder.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_confounder_files/figure-html/conf_assoc_plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_confounder_files/figure-html/dorea_plot-1.png" but not available.
--- finished re-building ‘SIAMCAT_confounder.Rmd’
--- re-building ‘SIAMCAT_holdout.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_holdout.Rmd’
--- re-building ‘SIAMCAT_meta.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_meta_files/figure-html/heatmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_meta_files/figure-html/plot_auroc-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_meta_files/figure-html/plot_weights_heatmap-1.png" but not available.
--- finished re-building ‘SIAMCAT_meta.Rmd’
--- re-building ‘SIAMCAT_ml_pitfalls.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/plot_auroc-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/hmp_samples-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/plot_results_db-1.png" but not available.
--- finished re-building ‘SIAMCAT_ml_pitfalls.Rmd’
+-+SIAMCAT_ml_pitfalls.html
Killed
--- re-building ‘SIAMCAT_read-in.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_read-in.Rmd’
--- re-building ‘SIAMCAT_vignette.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_vignette.Rmd’
SUMMARY: processing the following file failed:
‘SIAMCAT_ml_pitfalls.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.
SIAMCAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SIAMCAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 | 0.011 | 0.000 | 0.015 | |
| add.meta.pred | 0.029 | 0.004 | 0.033 | |
| assign-associations | 0.009 | 0.000 | 0.009 | |
| assign-data_split | 0.005 | 0.004 | 0.009 | |
| assign-eval_data | 0.009 | 0.000 | 0.010 | |
| assign-filt_feat | 0.005 | 0.004 | 0.009 | |
| assign-label | 0.009 | 0.000 | 0.009 | |
| assign-meta | 0.035 | 0.000 | 0.036 | |
| assign-model_list | 28.822 | 0.256 | 29.104 | |
| assign-norm_feat | 0.010 | 0.000 | 0.011 | |
| assign-orig_feat | 0.015 | 0.000 | 0.015 | |
| assign-physeq | 0.009 | 0.000 | 0.009 | |
| assign-pred_matrix | 0.005 | 0.004 | 0.009 | |
| assoc_param-methods | 0.007 | 0.000 | 0.007 | |
| association.plot | 0.308 | 0.008 | 0.328 | |
| associations-methods | 0.007 | 0.004 | 0.011 | |
| check.associations | 2.528 | 0.001 | 2.554 | |
| check.confounders | 0.557 | 0.012 | 0.585 | |
| create.data.split | 0.028 | 0.000 | 0.029 | |
| create.label | 0.002 | 0.000 | 0.003 | |
| data_split-methods | 0.007 | 0.000 | 0.007 | |
| eval_data-methods | 0.007 | 0.000 | 0.008 | |
| evaluate.predictions | 0.029 | 0.000 | 0.029 | |
| feature_type-methods | 0.007 | 0.000 | 0.007 | |
| feature_weights-methods | 0.007 | 0.000 | 0.007 | |
| filt_feat-methods | 0.007 | 0.000 | 0.007 | |
| filt_params-methods | 0.007 | 0.000 | 0.007 | |
| filter.features | 0.042 | 0.000 | 0.041 | |
| filter.label | 0.009 | 0.000 | 0.009 | |
| get.filt_feat.matrix | 0.007 | 0.000 | 0.008 | |
| get.norm_feat.matrix | 0.008 | 0.000 | 0.007 | |
| get.orig_feat.matrix | 0.007 | 0.000 | 0.007 | |
| label-methods | 0.008 | 0.000 | 0.007 | |
| make.predictions | 28.991 | 0.216 | 29.224 | |
| meta-methods | 0.020 | 0.004 | 0.032 | |
| model.evaluation.plot | 0.025 | 0.012 | 0.051 | |
| model.interpretation.plot | 27.707 | 0.563 | 29.496 | |
| model_list-methods | 0.008 | 0.000 | 0.008 | |
| model_type-methods | 0.003 | 0.004 | 0.007 | |
| models-methods | 0.008 | 0.000 | 0.007 | |
| norm_feat-methods | 0.007 | 0.000 | 0.007 | |
| norm_params-methods | 0.007 | 0.000 | 0.007 | |
| normalize.features | 0.017 | 0.000 | 0.018 | |
| orig_feat-methods | 0.007 | 0.000 | 0.008 | |
| physeq-methods | 0.011 | 0.000 | 0.011 | |
| pred_matrix-methods | 0.007 | 0.000 | 0.007 | |
| read.label | 0.010 | 0.000 | 0.011 | |
| read.lefse | 0.907 | 0.004 | 0.912 | |
| select.samples | 0.067 | 0.008 | 0.075 | |
| siamcat | 0.312 | 0.004 | 0.317 | |
| siamcat.to.lefse | 0.017 | 0.004 | 0.021 | |
| siamcat.to.maaslin | 0.023 | 0.000 | 0.023 | |
| summarize.features | 2.696 | 0.012 | 2.709 | |
| train.model | 27.904 | 0.164 | 28.083 | |
| validate.data | 0.025 | 0.000 | 0.025 | |
| volcano.plot | 0.011 | 0.004 | 0.017 | |
| weight_matrix-methods | 0.007 | 0.000 | 0.007 | |