| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:27 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 scFeatureFilter package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scFeatureFilter.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1784/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scFeatureFilter 1.19.0 (landing page) Guillaume Devailly
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: scFeatureFilter |
| Version: 1.19.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scFeatureFilter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scFeatureFilter_1.19.0.tar.gz |
| StartedAt: 2023-02-07 14:45:00 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 14:55:45 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 644.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: scFeatureFilter.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scFeatureFilter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scFeatureFilter_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘scFeatureFilter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scFeatureFilter’ version ‘1.19.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scFeatureFilter’ 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
2019-12-06: The vignette is no longer failing
* 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 ... 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
plot_correlations_distributions 81.781 1.193 97.618
plot_metric 71.699 0.142 78.148
sc_feature_filter 70.274 0.152 79.201
bin_scdata 8.016 0.577 15.750
plot_mean_variance 6.364 0.056 7.152
get_mean_median 0.219 0.566 5.097
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘Introduction.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Introduction.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/vign_test/scFeatureFilter/vignettes/Introduction_files/figure-html/unnamed-chunk-6-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/vign_test/scFeatureFilter/vignettes/Introduction_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/vign_test/scFeatureFilter/vignettes/Introduction_files/figure-html/unnamed-chunk-9-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/vign_test/scFeatureFilter/vignettes/Introduction_files/figure-html/unnamed-chunk-11-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/vign_test/scFeatureFilter/vignettes/Introduction_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/vign_test/scFeatureFilter/vignettes/Introduction_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/vign_test/scFeatureFilter/vignettes/Introduction_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/vign_test/scFeatureFilter/vignettes/Introduction_files/figure-html/unnamed-chunk-15-1.png" but not available.
Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/scFeatureFilter.Rcheck/00check.log’
for details.
scFeatureFilter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scFeatureFilter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘scFeatureFilter’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (scFeatureFilter)
scFeatureFilter.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(dplyr)
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(scFeatureFilter)
>
> test_check("scFeatureFilter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
10.139 0.363 11.844
scFeatureFilter.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(dplyr)
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(scFeatureFilter)
>
> test_check("scFeatureFilter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
10.185 0.325 12.324
scFeatureFilter.Rcheck/scFeatureFilter-Ex.timings
| name | user | system | elapsed | |
| bin_scdata | 8.016 | 0.577 | 15.750 | |
| calculate_cvs | 0.069 | 0.023 | 0.184 | |
| correlate_windows | 0.139 | 0.032 | 0.209 | |
| correlations_to_densities | 0.263 | 0.024 | 0.349 | |
| define_top_genes | 0.182 | 0.000 | 0.394 | |
| determine_bin_cutoff | 0.065 | 0.000 | 0.133 | |
| filter_expression_table | 0.150 | 0.014 | 0.663 | |
| get_mean_median | 0.219 | 0.566 | 5.097 | |
| plot_correlations_distributions | 81.781 | 1.193 | 97.618 | |
| plot_mean_variance | 6.364 | 0.056 | 7.152 | |
| plot_metric | 71.699 | 0.142 | 78.148 | |
| plot_top_window_autocor | 1.794 | 0.000 | 2.071 | |
| sc_feature_filter | 70.274 | 0.152 | 79.201 | |