| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:49 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 scifer package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1783/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scifer 1.1.0 (landing page) Rodrigo Arcoverde Cerveira
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: scifer |
| Version: 1.1.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scifer.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scifer_1.1.0.tar.gz |
| StartedAt: 2022-12-29 03:18:07 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 03:23:20 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 313.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scifer.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scifer.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scifer_1.1.0.tar.gz
###
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##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/scifer.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scifer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scifer' version '1.1.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'scifer' 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 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
summarise_quality 50.70 0.32 51.23
secondary_peaks 11.51 0.12 11.64
summarise_abi_file 10.88 0.10 10.97
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* 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: OK
scifer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL scifer ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'scifer' ... ** using staged installation ** R ** 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 (scifer)
scifer.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(scifer)
>
> test_check("scifer")
processing file: HC_report.Rmd
inline R code fragments
label: setup (with options)
List of 1
$ include: logi FALSE
ordinary text without R code
label: logo (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: load_packages (with options)
List of 4
$ include: logi FALSE
$ warning: logi FALSE
$ echo : logi FALSE
$ message: logi FALSE
ordinary text without R code
label: dataset (with options)
List of 2
$ echo : logi FALSE
$ results: chr "hide"
ordinary text without R code
label: error_checkings (with options)
List of 3
$ results: chr "hide"
$ echo : logi FALSE
$ warning: logi FALSE
ordinary text without R code
label: filtering (with options)
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$ echo : logi FALSE
$ warning: logi FALSE
ordinary text without R code
label: CDR3 (with options)
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$ echo : logi FALSE
$ include: logi FALSE
$ warning: logi FALSE
ordinary text without R code
label: plot_folder_name_quality (with options)
List of 3
$ echo : logi FALSE
$ warning : logi FALSE
$ fig.align: chr "center"
ordinary text without R code
label: plot_quality (with options)
List of 3
$ echo : logi FALSE
$ warning : logi FALSE
$ fig.align: chr "center"
ordinary text without R code
label: plate_quality (with options)
List of 4
$ echo : logi FALSE
$ warning : logi FALSE
$ quietly : logi TRUE
$ fig.align: chr "center"
ordinary text without R code
label: add_sequence (with options)
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$ echo : logi FALSE
$ include: logi FALSE
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label: plot_CDR3 (with options)
List of 3
$ echo : logi FALSE
$ warning : logi FALSE
$ fig.align: chr "center"
ordinary text without R code
label: chromatogram (with options)
List of 3
$ echo : logi FALSE
$ eval : logi FALSE
$ include: logi FALSE
ordinary text without R code
label: fcs_processing (with options)
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$ warning: logi FALSE
ordinary text without R code
label: processing_flow_data (with options)
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$ warning: logi FALSE
$ include: logi TRUE
$ eval : logi TRUE
ordinary text without R code
label: specificity (with options)
List of 3
$ echo : logi FALSE
$ warning: logi FALSE
$ include: logi FALSE
ordinary text without R code
label: fasta (with options)
List of 2
$ echo : logi FALSE
$ include: logi FALSE
ordinary text without R code
label: loop_report (with options)
List of 2
$ echo : logi FALSE
$ include: logi FALSE
ordinary text without R code
label: unnamed-chunk-1
output file: HC_report.knit.md
"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS HC_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc1622851fe6bbc.html --lua-filter "F:\biocbuild\bbs-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "F:\biocbuild\bbs-3.17-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpUDnE9f\rmarkdown-str16228368c5f2e.html"
Output created: F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/RtmpUDnE9f/QC_report.html
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 36 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 36 ]
>
> proc.time()
user system elapsed
136.32 2.79 141.09
scifer.Rcheck/scifer-Ex.timings
| name | user | system | elapsed | |
| df_to_fasta | 0.03 | 0.00 | 0.03 | |
| fcs_plot | 0.32 | 0.14 | 0.45 | |
| fcs_processing | 0.27 | 0.08 | 0.34 | |
| quality_report | 0 | 0 | 0 | |
| secondary_peaks | 11.51 | 0.12 | 11.64 | |
| summarise_abi_file | 10.88 | 0.10 | 10.97 | |
| summarise_quality | 50.70 | 0.32 | 51.23 | |