Jakob Wirbel
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/SIAMCAT |
| git_branch: master |
| git_last_commit: 3f5f13f |
| git_last_commit_date: 2021-10-26 12:44:50 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:41 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? 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 1792/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIAMCAT 1.15.0 (landing page) Jakob Wirbel
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SIAMCAT |
| Version: 1.15.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SIAMCAT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SIAMCAT_1.15.0.tar.gz |
| StartedAt: 2022-03-17 20:16:50 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:20:08 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 198.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIAMCAT.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SIAMCAT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SIAMCAT_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SIAMCAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIAMCAT' version '1.15.0'
* 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 whether package 'SIAMCAT' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
extdata 2.1Mb
help 2.1Mb
* 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 17.25 0.14 17.39
* 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: 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck/00check.log'
for details.
SIAMCAT.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SIAMCAT
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'SIAMCAT'
finding HTML links ... done
SIAMCAT-package html
accessSlot html
add.meta.pred html
assign-associations html
assign-data_split html
assign-eval_data html
assign-filt_feat html
assign-label html
assign-meta html
assign-model_list html
assign-norm_feat html
assign-orig_feat html
assign-physeq html
assign-pred_matrix html
assoc_param-methods html
associations-methods html
check.associations html
check.confounders html
create.data.split html
create.label html
data_split-methods html
eval_data-methods html
evaluate.predictions html
feat.crc.zeller html
feature_type-methods html
feature_weights-methods html
filt_feat-methods html
filt_params-methods html
filter.features html
filter.label html
get.component.classes html
get.filt_feat.matrix html
get.norm_feat.matrix html
get.orig_feat.matrix html
label-methods html
make.predictions html
meta-methods html
meta.crc.zeller html
model.evaluation.plot html
model.interpretation.plot html
model_list-methods html
model_type-methods html
models-methods html
norm_feat-methods html
norm_params-methods html
normalize.features html
orig_feat-methods html
parse.label.header html
physeq-methods html
pred_matrix-methods html
read.label html
read.lefse html
select.samples html
show-methods html
siamcat-class html
siamcat html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-SIAMCAT/00new/SIAMCAT/help/siamcat.html
siamcat.to.lefse html
siamcat.to.maaslin html
siamcat_example html
summarize.features html
finding level-2 HTML links ... done
train.model html
validate.data html
weight_matrix-methods html
*** 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)
Making 'packages.html' ... done
SIAMCAT.Rcheck/SIAMCAT-Ex.timings
| name | user | system | elapsed | |
| accessSlot | 0.01 | 0.00 | 0.02 | |
| add.meta.pred | 0.05 | 0.00 | 0.05 | |
| assign-associations | 0.02 | 0.00 | 0.01 | |
| assign-data_split | 0.42 | 0.02 | 0.44 | |
| assign-eval_data | 0.02 | 0.00 | 0.01 | |
| assign-filt_feat | 0.01 | 0.00 | 0.02 | |
| assign-label | 0.03 | 0.00 | 0.03 | |
| assign-meta | 0.05 | 0.00 | 0.05 | |
| assign-model_list | 0.02 | 0.00 | 0.01 | |
| assign-norm_feat | 0.03 | 0.00 | 0.03 | |
| assign-orig_feat | 0.03 | 0.00 | 0.04 | |
| assign-physeq | 0.01 | 0.00 | 0.01 | |
| assign-pred_matrix | 0.03 | 0.00 | 0.03 | |
| assoc_param-methods | 0.02 | 0.00 | 0.02 | |
| associations-methods | 0.02 | 0.01 | 0.03 | |
| check.associations | 0.26 | 0.00 | 0.27 | |
| check.confounders | 0.41 | 0.04 | 0.43 | |
| create.data.split | 0.03 | 0.00 | 0.03 | |
| create.label | 0.00 | 0.01 | 0.02 | |
| data_split-methods | 0.01 | 0.00 | 0.02 | |
| eval_data-methods | 0.02 | 0.00 | 0.01 | |
| evaluate.predictions | 0.02 | 0.02 | 0.03 | |
| feature_type-methods | 0.01 | 0.00 | 0.02 | |
| feature_weights-methods | 0.02 | 0.01 | 0.03 | |
| filt_feat-methods | 0.03 | 0.00 | 0.03 | |
| filt_params-methods | 0.03 | 0.00 | 0.03 | |
| filter.features | 0.02 | 0.00 | 0.02 | |
| filter.label | 0.01 | 0.00 | 0.01 | |
| get.filt_feat.matrix | 0.02 | 0.03 | 0.05 | |
| get.norm_feat.matrix | 0.03 | 0.00 | 0.03 | |
| get.orig_feat.matrix | 0.01 | 0.00 | 0.02 | |
| label-methods | 0.02 | 0.00 | 0.01 | |
| make.predictions | 0.18 | 0.00 | 0.17 | |
| meta-methods | 0.03 | 0.02 | 0.05 | |
| model.evaluation.plot | 0.03 | 0.00 | 0.03 | |
| model.interpretation.plot | 0.08 | 0.03 | 0.11 | |
| model_list-methods | 0.03 | 0.00 | 0.03 | |
| model_type-methods | 0.00 | 0.02 | 0.01 | |
| models-methods | 0.03 | 0.01 | 0.05 | |
| norm_feat-methods | 0.02 | 0.00 | 0.02 | |
| norm_params-methods | 0.03 | 0.00 | 0.03 | |
| normalize.features | 0.04 | 0.00 | 0.04 | |
| orig_feat-methods | 0.02 | 0.02 | 0.04 | |
| physeq-methods | 0.03 | 0.00 | 0.03 | |
| pred_matrix-methods | 0.02 | 0.00 | 0.01 | |
| read.label | 0.00 | 0.01 | 0.02 | |
| read.lefse | 1.23 | 0.05 | 1.28 | |
| select.samples | 0.08 | 0.00 | 0.08 | |
| siamcat | 0.34 | 0.00 | 0.35 | |
| siamcat.to.lefse | 0.08 | 0.01 | 0.09 | |
| siamcat.to.maaslin | 0.06 | 0.00 | 0.06 | |
| summarize.features | 2.03 | 0.22 | 2.25 | |
| train.model | 17.25 | 0.14 | 17.39 | |
| validate.data | 0.04 | 0.00 | 0.04 | |
| weight_matrix-methods | 0.01 | 0.00 | 0.01 | |