| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:18 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 ScreenR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ScreenR.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 1819/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.0.0 (landing page) Emanuel Michele Soda
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ScreenR |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ScreenR_1.0.0.tar.gz |
| StartedAt: 2023-04-10 23:51:36 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:56:25 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 288.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScreenR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ScreenR_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/ScreenR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ScreenR’ 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 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_zscore_distribution 38.263 0.652 38.915
plot_barcode_trend 37.407 0.528 37.936
compute_metrics 21.386 1.683 23.072
find_robust_zscore_hit 17.763 0.568 18.331
find_zscore_hit 17.694 0.349 18.042
* 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 ...
‘Analysis_Example.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
ScreenR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘ScreenR’ ... ** using staged installation ** R ** data ** 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 (ScreenR)
ScreenR.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(ScreenR)
Welcome to ScreenR
--------------------------
See ?ScreenR for a list of
available functions.
Enjoy!
>
> test_check("ScreenR")
ScreenR count table containing:
5320 rows
15 columns
ScreenR annotation table containing:
5320 rows
5 columns
ScreenR normalized count table containing:
5320 rows
15 columns
ScreenR normalized data table containing:
74480 rows
9 columns
ScreenR annotation table containing:
5320 rows
5 columns
ScreenR annotation table containing:
5320 rows
5 columns
ScreenR count table containing:
5320 rows
15 columns
ScreenR count table containing:
5320 rows
15 columns
ScreenR normalized count table containing:
5320 rows
15 columns
ScreenR normalized count table containing:
5320 rows
15 columns
ScreenR normalized data table containing:
74480 rows
9 columns
ScreenR normalized data table containing:
74480 rows
9 columns
Using classic mode.
[ FAIL 0 | WARN 253 | SKIP 0 | PASS 64 ]
[ FAIL 0 | WARN 253 | SKIP 0 | PASS 64 ]
>
> proc.time()
user system elapsed
22.640 0.449 23.075
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.169 | 0.019 | 0.189 | |
| compute_data_table | 0.234 | 0.005 | 0.237 | |
| compute_explained_variance | 0.023 | 0.004 | 0.028 | |
| compute_metrics | 21.386 | 1.683 | 23.072 | |
| compute_slope | 0.055 | 0.000 | 0.054 | |
| count_mapped_reads | 0.043 | 0.000 | 0.043 | |
| create_edger_obj | 0.050 | 0.005 | 0.054 | |
| create_screenr_object | 0.039 | 0.000 | 0.039 | |
| filter_by_slope | 0.135 | 0.000 | 0.135 | |
| filter_by_variance | 1.062 | 0.000 | 1.062 | |
| find_camera_hit | 1.137 | 0.011 | 1.149 | |
| find_common_hit | 0.041 | 0.000 | 0.041 | |
| find_roast_hit | 1.776 | 0.007 | 1.784 | |
| find_robust_zscore_hit | 17.763 | 0.568 | 18.331 | |
| find_zscore_hit | 17.694 | 0.349 | 18.042 | |
| get_annotation_table | 0.014 | 0.000 | 0.014 | |
| get_count_table | 0.076 | 0.000 | 0.076 | |
| get_data_table | 0.026 | 0.000 | 0.026 | |
| get_groups | 0.001 | 0.000 | 0.000 | |
| get_normalized_count_table | 0.04 | 0.00 | 0.04 | |
| get_replicates | 0 | 0 | 0 | |
| mapped_reads | 0.068 | 0.000 | 0.069 | |
| normalize_data | 0.043 | 0.000 | 0.043 | |
| plot_barcode_hit | 1.188 | 0.008 | 1.196 | |
| plot_barcode_lost | 0.332 | 0.004 | 0.337 | |
| plot_barcode_lost_for_gene | 1.272 | 0.004 | 1.277 | |
| plot_barcode_trend | 37.407 | 0.528 | 37.936 | |
| plot_boxplot | 0.422 | 0.000 | 0.422 | |
| plot_common_hit | 0.191 | 0.007 | 0.201 | |
| plot_explained_variance | 0.387 | 0.000 | 0.387 | |
| plot_mapped_reads | 0.184 | 0.000 | 0.185 | |
| plot_mapped_reads_distribution | 2.263 | 0.004 | 2.268 | |
| plot_mds | 0.409 | 0.003 | 0.412 | |
| plot_trend | 1.702 | 0.005 | 1.706 | |
| plot_zscore_distribution | 38.263 | 0.652 | 38.915 | |
| remove_all_zero_row | 0.015 | 0.000 | 0.016 | |
| set_annotation_table | 0.164 | 0.000 | 0.164 | |
| set_count_table | 0.141 | 0.000 | 0.140 | |
| set_data_table | 0.141 | 0.000 | 0.141 | |
| set_groups | 0.139 | 0.000 | 0.139 | |
| set_normalized_count_table | 0.174 | 0.000 | 0.174 | |
| set_replicates | 0.124 | 0.000 | 0.125 | |