Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:36:23 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 |
Package 1944/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SIAMCAT 2.6.0 (landing page) Jakob Wirbel
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SIAMCAT package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SIAMCAT |
Version: 2.6.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SIAMCAT_2.6.0.tar.gz |
StartedAt: 2024-03-28 02:43:26 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 02:51:26 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 479.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SIAMCAT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SIAMCAT_2.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SIAMCAT.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘SIAMCAT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SIAMCAT’ version ‘2.6.0’ * package encoding: UTF-8 * 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 loading without being on the library search path ... 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 assign-model_list 21.582 0.392 21.975 model.interpretation.plot 21.094 0.200 21.294 make.predictions 20.639 0.268 20.907 train.model 20.242 0.203 20.445 * 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 ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/SIAMCAT.Rcheck/00check.log’ for details.
SIAMCAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SIAMCAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 | 0.009 | 0.000 | 0.009 | |
add.meta.pred | 0.032 | 0.000 | 0.032 | |
assign-associations | 0.007 | 0.000 | 0.007 | |
assign-data_split | 0.007 | 0.000 | 0.007 | |
assign-eval_data | 0.004 | 0.004 | 0.008 | |
assign-filt_feat | 0.008 | 0.000 | 0.008 | |
assign-label | 0.008 | 0.000 | 0.008 | |
assign-meta | 0.026 | 0.000 | 0.026 | |
assign-model_list | 21.582 | 0.392 | 21.975 | |
assign-norm_feat | 0.007 | 0.000 | 0.007 | |
assign-orig_feat | 0.011 | 0.000 | 0.011 | |
assign-physeq | 0.003 | 0.003 | 0.007 | |
assign-pred_matrix | 0.007 | 0.000 | 0.007 | |
assoc_param-methods | 0.005 | 0.000 | 0.005 | |
association.plot | 0.200 | 0.008 | 0.208 | |
associations-methods | 0.008 | 0.000 | 0.008 | |
check.associations | 0.01 | 0.00 | 0.01 | |
check.confounders | 0.411 | 0.000 | 0.412 | |
create.data.split | 0.02 | 0.00 | 0.02 | |
create.label | 0.002 | 0.000 | 0.003 | |
data_split-methods | 0.005 | 0.000 | 0.005 | |
eval_data-methods | 0.006 | 0.000 | 0.006 | |
evaluate.predictions | 1.456 | 0.000 | 1.456 | |
feature_type-methods | 0.002 | 0.004 | 0.005 | |
feature_weights-methods | 0.002 | 0.004 | 0.006 | |
filt_feat-methods | 0.002 | 0.004 | 0.006 | |
filt_params-methods | 0.005 | 0.000 | 0.005 | |
filter.features | 0.013 | 0.000 | 0.013 | |
filter.label | 0.008 | 0.000 | 0.007 | |
get.filt_feat.matrix | 0.006 | 0.000 | 0.006 | |
get.norm_feat.matrix | 0.002 | 0.003 | 0.006 | |
get.orig_feat.matrix | 0.002 | 0.005 | 0.006 | |
label-methods | 0.028 | 0.000 | 0.028 | |
make.predictions | 20.639 | 0.268 | 20.907 | |
meta-methods | 0.023 | 0.000 | 0.022 | |
model.evaluation.plot | 0.018 | 0.008 | 0.026 | |
model.interpretation.plot | 21.094 | 0.200 | 21.294 | |
model_list-methods | 0.006 | 0.000 | 0.006 | |
model_type-methods | 0.006 | 0.000 | 0.006 | |
models-methods | 0.006 | 0.000 | 0.005 | |
norm_feat-methods | 0.006 | 0.000 | 0.006 | |
norm_params-methods | 0.006 | 0.000 | 0.006 | |
normalize.features | 0.015 | 0.000 | 0.014 | |
orig_feat-methods | 0.006 | 0.000 | 0.006 | |
physeq-methods | 0.009 | 0.000 | 0.010 | |
pred_matrix-methods | 0.006 | 0.000 | 0.006 | |
read.label | 0.004 | 0.003 | 0.007 | |
read.lefse | 0.560 | 0.013 | 0.571 | |
select.samples | 0.056 | 0.000 | 0.055 | |
siamcat | 0.308 | 0.012 | 0.320 | |
siamcat.to.lefse | 0.023 | 0.000 | 0.023 | |
siamcat.to.maaslin | 0.021 | 0.004 | 0.025 | |
summarize.features | 2.253 | 0.068 | 2.322 | |
train.model | 20.242 | 0.203 | 20.445 | |
validate.data | 0.02 | 0.00 | 0.02 | |
volcano.plot | 0.013 | 0.000 | 0.013 | |
weight_matrix-methods | 0.003 | 0.003 | 0.006 | |