| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:40 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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: - 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 1827/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.3.0 (landing page) Emanuel Michele Soda
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ScreenR |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ScreenR_1.3.0.tar.gz |
| StartedAt: 2023-05-10 04:10:19 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 04:17:22 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 422.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScreenR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ScreenR_1.3.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ScreenR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* 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 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_barcode_trend 57.117 1.704 58.823
plot_zscore_distribution 56.991 1.180 58.172
compute_metrics 32.935 1.692 34.630
find_zscore_hit 28.293 1.067 29.362
find_robust_zscore_hit 25.733 0.765 26.498
* 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-3.17-bioc/R/bin/R CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "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(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
33.079 0.536 33.597
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.199 | 0.012 | 0.211 | |
| compute_data_table | 0.281 | 0.024 | 0.305 | |
| compute_explained_variance | 0.034 | 0.008 | 0.041 | |
| compute_metrics | 32.935 | 1.692 | 34.630 | |
| compute_slope | 0.066 | 0.000 | 0.067 | |
| count_mapped_reads | 0.055 | 0.003 | 0.059 | |
| create_edger_obj | 0.037 | 0.000 | 0.037 | |
| create_screenr_object | 0.054 | 0.004 | 0.059 | |
| filter_by_slope | 0.174 | 0.007 | 0.182 | |
| filter_by_variance | 1.442 | 0.000 | 1.442 | |
| find_camera_hit | 1.569 | 0.004 | 1.573 | |
| find_common_hit | 0.038 | 0.000 | 0.038 | |
| find_roast_hit | 2.369 | 0.003 | 2.373 | |
| find_robust_zscore_hit | 25.733 | 0.765 | 26.498 | |
| find_zscore_hit | 28.293 | 1.067 | 29.362 | |
| get_annotation_table | 0.021 | 0.000 | 0.020 | |
| get_count_table | 0.113 | 0.004 | 0.116 | |
| get_data_table | 0.036 | 0.000 | 0.037 | |
| get_groups | 0.001 | 0.000 | 0.001 | |
| get_normalized_count_table | 0.052 | 0.004 | 0.056 | |
| get_replicates | 0.001 | 0.000 | 0.000 | |
| mapped_reads | 0.097 | 0.000 | 0.097 | |
| normalize_data | 0.064 | 0.000 | 0.064 | |
| plot_barcode_hit | 1.861 | 0.048 | 1.910 | |
| plot_barcode_lost | 0.484 | 0.012 | 0.496 | |
| plot_barcode_lost_for_gene | 1.988 | 0.020 | 2.009 | |
| plot_barcode_trend | 57.117 | 1.704 | 58.823 | |
| plot_boxplot | 0.505 | 0.000 | 0.505 | |
| plot_common_hit | 0.259 | 0.000 | 0.260 | |
| plot_explained_variance | 0.499 | 0.004 | 0.502 | |
| plot_mapped_reads | 0.251 | 0.004 | 0.256 | |
| plot_mapped_reads_distribution | 2.916 | 0.024 | 2.940 | |
| plot_mds | 0.496 | 0.008 | 0.504 | |
| plot_trend | 1.875 | 0.020 | 1.896 | |
| plot_zscore_distribution | 56.991 | 1.180 | 58.172 | |
| remove_all_zero_row | 0.016 | 0.000 | 0.016 | |
| set_annotation_table | 0.168 | 0.000 | 0.168 | |
| set_count_table | 0.179 | 0.000 | 0.179 | |
| set_data_table | 0.169 | 0.000 | 0.169 | |
| set_groups | 0.17 | 0.00 | 0.17 | |
| set_normalized_count_table | 0.234 | 0.004 | 0.238 | |
| set_replicates | 0.171 | 0.000 | 0.171 | |