Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1934/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SIAMCAT 2.11.0 (landing page) Jakob Wirbel
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 2.11.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SIAMCAT_2.11.0.tar.gz |
StartedAt: 2024-12-24 02:13:38 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 02:21:30 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 471.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SIAMCAT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SIAMCAT_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SIAMCAT.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘SIAMCAT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SIAMCAT’ version ‘2.11.0’ * 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 ... 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 code 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: check.associations.Rd: lmerTest summarize.features.Rd: phyloseq train.model.Rd: mlr3learners, glmnet, LiblineaR Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 21.639 0.524 22.166 make.predictions 21.644 0.314 21.960 model.interpretation.plot 21.248 0.270 21.520 train.model 20.773 0.147 20.922 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/SIAMCAT.Rcheck/00check.log’ for details.
SIAMCAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SIAMCAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 | 0.003 | 0.006 | 0.009 | |
add.meta.pred | 0.022 | 0.001 | 0.023 | |
assign-associations | 0.005 | 0.001 | 0.005 | |
assign-data_split | 0.006 | 0.000 | 0.005 | |
assign-eval_data | 0.005 | 0.001 | 0.005 | |
assign-filt_feat | 0.005 | 0.001 | 0.006 | |
assign-label | 0.005 | 0.001 | 0.006 | |
assign-meta | 0.023 | 0.001 | 0.024 | |
assign-model_list | 21.639 | 0.524 | 22.166 | |
assign-norm_feat | 0.015 | 0.004 | 0.019 | |
assign-orig_feat | 0.012 | 0.001 | 0.013 | |
assign-physeq | 0.004 | 0.001 | 0.007 | |
assign-pred_matrix | 0.004 | 0.001 | 0.007 | |
assoc_param-methods | 0.004 | 0.001 | 0.005 | |
association.plot | 0.197 | 0.005 | 0.203 | |
associations-methods | 0.006 | 0.002 | 0.008 | |
check.associations | 0.008 | 0.001 | 0.009 | |
check.confounders | 0.424 | 0.009 | 0.434 | |
create.data.split | 0.018 | 0.001 | 0.019 | |
create.label | 0.002 | 0.001 | 0.002 | |
data_split-methods | 0.004 | 0.000 | 0.004 | |
eval_data-methods | 0.004 | 0.000 | 0.004 | |
evaluate.predictions | 1.509 | 0.008 | 1.517 | |
feature_type-methods | 0.004 | 0.000 | 0.004 | |
feature_weights-methods | 0.003 | 0.000 | 0.004 | |
filt_feat-methods | 0.004 | 0.000 | 0.004 | |
filt_params-methods | 0.003 | 0.002 | 0.004 | |
filter.features | 0.013 | 0.000 | 0.012 | |
filter.label | 0.004 | 0.001 | 0.005 | |
get.filt_feat.matrix | 0.005 | 0.001 | 0.004 | |
get.norm_feat.matrix | 0.004 | 0.001 | 0.004 | |
get.orig_feat.matrix | 0.004 | 0.000 | 0.005 | |
label-methods | 0.017 | 0.000 | 0.017 | |
make.predictions | 21.644 | 0.314 | 21.960 | |
meta-methods | 0.019 | 0.001 | 0.019 | |
model.evaluation.plot | 0.023 | 0.002 | 0.025 | |
model.interpretation.plot | 21.248 | 0.270 | 21.520 | |
model_list-methods | 0.002 | 0.002 | 0.005 | |
model_type-methods | 0.004 | 0.001 | 0.004 | |
models-methods | 0.003 | 0.002 | 0.004 | |
norm_feat-methods | 0.005 | 0.000 | 0.005 | |
norm_params-methods | 0.005 | 0.000 | 0.005 | |
normalize.features | 0.010 | 0.002 | 0.012 | |
orig_feat-methods | 0.005 | 0.000 | 0.005 | |
physeq-methods | 0.006 | 0.001 | 0.008 | |
pred_matrix-methods | 0.003 | 0.002 | 0.004 | |
read.label | 0.005 | 0.002 | 0.007 | |
read.lefse | 0.545 | 0.016 | 0.563 | |
select.samples | 0.048 | 0.000 | 0.048 | |
siamcat | 0.269 | 0.010 | 0.278 | |
siamcat.to.lefse | 0.014 | 0.001 | 0.015 | |
siamcat.to.maaslin | 0.017 | 0.000 | 0.017 | |
summarize.features | 1.861 | 0.073 | 1.937 | |
train.model | 20.773 | 0.147 | 20.922 | |
validate.data | 0.016 | 0.000 | 0.017 | |
volcano.plot | 0.009 | 0.000 | 0.009 | |
weight_matrix-methods | 0.003 | 0.001 | 0.004 | |