| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:41 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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To the developers/maintainers of the ScreenR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1832/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.3.0 (landing page) Emanuel Michele Soda
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: ScreenR |
| Version: 1.3.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ScreenR_1.3.0.tar.gz |
| StartedAt: 2023-06-06 06:32:11 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 06:39:13 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 422.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScreenR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ScreenR_1.3.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ScreenR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.3.0’
* 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 startup messages can be suppressed ... 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 58.108 0.563 58.774
plot_barcode_trend 56.292 0.375 56.768
compute_metrics 33.838 1.086 34.982
find_zscore_hit 27.487 0.315 27.849
find_robust_zscore_hit 26.267 0.488 26.803
* 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/R/R-4.3.0/bin/R CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
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(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
33.593 0.365 34.007
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.196 | 0.004 | 0.201 | |
| compute_data_table | 0.280 | 0.024 | 0.304 | |
| compute_explained_variance | 0.033 | 0.003 | 0.037 | |
| compute_metrics | 33.838 | 1.086 | 34.982 | |
| compute_slope | 0.075 | 0.000 | 0.076 | |
| count_mapped_reads | 0.062 | 0.000 | 0.062 | |
| create_edger_obj | 0.038 | 0.000 | 0.038 | |
| create_screenr_object | 0.055 | 0.000 | 0.056 | |
| filter_by_slope | 0.189 | 0.000 | 0.189 | |
| filter_by_variance | 1.452 | 0.000 | 1.455 | |
| find_camera_hit | 1.598 | 0.004 | 1.605 | |
| find_common_hit | 0.051 | 0.000 | 0.051 | |
| find_roast_hit | 2.449 | 0.000 | 2.453 | |
| find_robust_zscore_hit | 26.267 | 0.488 | 26.803 | |
| find_zscore_hit | 27.487 | 0.315 | 27.849 | |
| get_annotation_table | 0.021 | 0.000 | 0.021 | |
| get_count_table | 0.108 | 0.000 | 0.108 | |
| get_data_table | 0.04 | 0.00 | 0.04 | |
| get_groups | 0.001 | 0.000 | 0.000 | |
| get_normalized_count_table | 0.059 | 0.000 | 0.058 | |
| get_replicates | 0 | 0 | 0 | |
| mapped_reads | 0.096 | 0.000 | 0.095 | |
| normalize_data | 0.062 | 0.000 | 0.062 | |
| plot_barcode_hit | 1.838 | 0.008 | 1.848 | |
| plot_barcode_lost | 0.465 | 0.008 | 0.474 | |
| plot_barcode_lost_for_gene | 2.058 | 0.000 | 2.061 | |
| plot_barcode_trend | 56.292 | 0.375 | 56.768 | |
| plot_boxplot | 0.542 | 0.004 | 0.547 | |
| plot_common_hit | 0.235 | 0.000 | 0.236 | |
| plot_explained_variance | 0.510 | 0.000 | 0.511 | |
| plot_mapped_reads | 0.266 | 0.000 | 0.266 | |
| plot_mapped_reads_distribution | 3.009 | 0.012 | 3.026 | |
| plot_mds | 0.538 | 0.000 | 0.539 | |
| plot_trend | 1.894 | 0.012 | 1.911 | |
| plot_zscore_distribution | 58.108 | 0.563 | 58.774 | |
| remove_all_zero_row | 0.015 | 0.000 | 0.016 | |
| set_annotation_table | 0.19 | 0.00 | 0.19 | |
| set_count_table | 0.189 | 0.000 | 0.188 | |
| set_data_table | 0.183 | 0.000 | 0.183 | |
| set_groups | 0.201 | 0.004 | 0.204 | |
| set_normalized_count_table | 0.248 | 0.004 | 0.253 | |
| set_replicates | 0.189 | 0.000 | 0.189 | |