Jakob Wirbel
| Snapshot Date: 2023-09-22 14:00:14 -0400 (Fri, 22 Sep 2023) |
| git_url: https://git.bioconductor.org/packages/SIAMCAT |
| git_branch: RELEASE_3_17 |
| git_last_commit: 026eb87 |
| git_last_commit_date: 2023-04-25 11:02:01 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-09-23 11:37:07 -0400 (Sat, 23 Sep 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4625 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4378 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4394 |
| 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 1907/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIAMCAT 2.4.0 (landing page) Jakob Wirbel
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | NA | |||||||||
|
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: 2.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIAMCAT_2.4.0.tar.gz |
| StartedAt: 2023-09-23 08:09:31 -0400 (Sat, 23 Sep 2023) |
| EndedAt: 2023-09-23 08:21:32 -0400 (Sat, 23 Sep 2023) |
| EllapsedTime: 721.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SIAMCAT.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIAMCAT_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.4.0’
* 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 ... WARNING
Found the following significant warnings:
Note: possible error in 'tune(method = "grid_search", ': unused argument (resolution = grid.size)
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... NOTE
train.model: possible error in tune(method = "grid_search", task =
task, learner = lrn.fold, resampling = rsmp("cv", folds = 5),
measures = msr(measure), resolution = grid.size): unused argument
(resolution = grid.size)
* 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 43.948 0.768 57.567
model.interpretation.plot 43.505 0.753 56.689
train.model 42.997 0.843 55.941
assign-model_list 41.535 1.032 51.194
summarize.features 4.624 0.237 6.199
* 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 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.
SIAMCAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIAMCAT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘SIAMCAT’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'tune(method = "grid_search", ': unused argument (resolution = grid.size) ** 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 | 0.014 | 0.010 | 0.029 | |
| add.meta.pred | 0.054 | 0.010 | 0.085 | |
| assign-associations | 0.012 | 0.005 | 0.022 | |
| assign-data_split | 0.013 | 0.003 | 0.023 | |
| assign-eval_data | 0.013 | 0.004 | 0.021 | |
| assign-filt_feat | 0.013 | 0.004 | 0.022 | |
| assign-label | 0.035 | 0.005 | 0.054 | |
| assign-meta | 0.054 | 0.003 | 0.068 | |
| assign-model_list | 41.535 | 1.032 | 51.194 | |
| assign-norm_feat | 0.012 | 0.002 | 0.017 | |
| assign-orig_feat | 0.022 | 0.003 | 0.029 | |
| assign-physeq | 0.013 | 0.002 | 0.020 | |
| assign-pred_matrix | 0.012 | 0.003 | 0.016 | |
| assoc_param-methods | 0.009 | 0.003 | 0.014 | |
| association.plot | 0.433 | 0.026 | 0.581 | |
| associations-methods | 0.015 | 0.004 | 0.027 | |
| check.associations | 3.532 | 0.042 | 4.718 | |
| check.confounders | 0.921 | 0.036 | 1.238 | |
| create.data.split | 0.048 | 0.002 | 0.064 | |
| create.label | 0.004 | 0.003 | 0.012 | |
| data_split-methods | 0.009 | 0.002 | 0.015 | |
| eval_data-methods | 0.010 | 0.005 | 0.020 | |
| evaluate.predictions | 0.049 | 0.005 | 0.070 | |
| feature_type-methods | 0.009 | 0.003 | 0.015 | |
| feature_weights-methods | 0.035 | 0.004 | 0.051 | |
| filt_feat-methods | 0.010 | 0.002 | 0.016 | |
| filt_params-methods | 0.010 | 0.003 | 0.017 | |
| filter.features | 0.031 | 0.004 | 0.040 | |
| filter.label | 0.012 | 0.002 | 0.018 | |
| get.filt_feat.matrix | 0.010 | 0.003 | 0.019 | |
| get.norm_feat.matrix | 0.009 | 0.003 | 0.015 | |
| get.orig_feat.matrix | 0.010 | 0.003 | 0.015 | |
| label-methods | 0.010 | 0.004 | 0.016 | |
| make.predictions | 43.948 | 0.768 | 57.567 | |
| meta-methods | 0.036 | 0.004 | 0.053 | |
| model.evaluation.plot | 0.042 | 0.013 | 0.079 | |
| model.interpretation.plot | 43.505 | 0.753 | 56.689 | |
| model_list-methods | 0.009 | 0.002 | 0.015 | |
| model_type-methods | 0.009 | 0.003 | 0.011 | |
| models-methods | 0.009 | 0.003 | 0.012 | |
| norm_feat-methods | 0.009 | 0.003 | 0.014 | |
| norm_params-methods | 0.009 | 0.003 | 0.015 | |
| normalize.features | 0.051 | 0.005 | 0.078 | |
| orig_feat-methods | 0.011 | 0.002 | 0.014 | |
| physeq-methods | 0.018 | 0.003 | 0.030 | |
| pred_matrix-methods | 0.011 | 0.003 | 0.015 | |
| read.label | 0.021 | 0.002 | 0.027 | |
| read.lefse | 1.493 | 0.049 | 2.040 | |
| select.samples | 0.120 | 0.003 | 0.156 | |
| siamcat | 0.453 | 0.028 | 0.633 | |
| siamcat.to.lefse | 0.040 | 0.004 | 0.053 | |
| siamcat.to.maaslin | 0.042 | 0.005 | 0.063 | |
| summarize.features | 4.624 | 0.237 | 6.199 | |
| train.model | 42.997 | 0.843 | 55.941 | |
| validate.data | 0.036 | 0.003 | 0.050 | |
| volcano.plot | 0.020 | 0.005 | 0.031 | |
| weight_matrix-methods | 0.009 | 0.002 | 0.014 | |