| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:50 -0000 (Wed, 01 Mar 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" | 4266 |
| 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: - 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 1809/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.1.0 (landing page) Emanuel Michele Soda
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ScreenR |
| Version: 1.1.0 |
| 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/library --timings ScreenR_1.1.0.tar.gz |
| StartedAt: 2023-02-28 14:50:35 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 14:57:58 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 442.5 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/library --timings ScreenR_1.1.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ScreenR.Rcheck’
* using R Under development (unstable) (2023-01-14 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 ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ 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 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 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 59.150 1.116 60.268
plot_barcode_trend 56.594 1.252 57.847
compute_metrics 33.982 1.348 35.335
find_zscore_hit 28.919 1.088 30.007
find_robust_zscore_hit 27.221 1.208 28.430
* 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/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) (2023-01-14 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(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
38.044 0.681 38.709
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.252 | 0.008 | 0.260 | |
| compute_data_table | 0.293 | 0.021 | 0.313 | |
| compute_explained_variance | 0.026 | 0.003 | 0.030 | |
| compute_metrics | 33.982 | 1.348 | 35.335 | |
| compute_slope | 0.093 | 0.000 | 0.093 | |
| count_mapped_reads | 0.066 | 0.000 | 0.065 | |
| create_edger_obj | 0.04 | 0.00 | 0.04 | |
| create_screenr_object | 0.055 | 0.000 | 0.055 | |
| filter_by_slope | 0.251 | 0.004 | 0.255 | |
| filter_by_variance | 1.499 | 0.003 | 1.503 | |
| find_camera_hit | 1.630 | 0.008 | 1.638 | |
| find_common_hit | 0.074 | 0.004 | 0.078 | |
| find_roast_hit | 2.491 | 0.000 | 2.491 | |
| find_robust_zscore_hit | 27.221 | 1.208 | 28.430 | |
| find_zscore_hit | 28.919 | 1.088 | 30.007 | |
| get_annotation_table | 0.03 | 0.00 | 0.03 | |
| get_count_table | 0.113 | 0.000 | 0.114 | |
| get_data_table | 0.036 | 0.000 | 0.036 | |
| get_groups | 0.001 | 0.000 | 0.000 | |
| get_normalized_count_table | 0.065 | 0.000 | 0.065 | |
| get_replicates | 0.000 | 0.000 | 0.001 | |
| mapped_reads | 0.099 | 0.004 | 0.103 | |
| normalize_data | 0.070 | 0.000 | 0.069 | |
| plot_barcode_hit | 1.858 | 0.024 | 1.882 | |
| plot_barcode_lost | 0.496 | 0.024 | 0.520 | |
| plot_barcode_lost_for_gene | 2.029 | 0.020 | 2.049 | |
| plot_barcode_trend | 56.594 | 1.252 | 57.847 | |
| plot_boxplot | 0.537 | 0.008 | 0.544 | |
| plot_common_hit | 0.694 | 0.000 | 0.695 | |
| plot_explained_variance | 0.535 | 0.000 | 0.534 | |
| plot_mapped_reads | 0.254 | 0.004 | 0.257 | |
| plot_mapped_reads_distribution | 2.826 | 0.048 | 2.874 | |
| plot_mds | 0.518 | 0.008 | 0.526 | |
| plot_trend | 1.970 | 0.016 | 1.987 | |
| plot_zscore_distribution | 59.150 | 1.116 | 60.268 | |
| remove_all_zero_row | 0.022 | 0.000 | 0.022 | |
| set_annotation_table | 0.209 | 0.000 | 0.209 | |
| set_count_table | 0.199 | 0.000 | 0.199 | |
| set_data_table | 0.199 | 0.000 | 0.199 | |
| set_groups | 0.204 | 0.000 | 0.204 | |
| set_normalized_count_table | 0.258 | 0.000 | 0.259 | |
| set_replicates | 0.198 | 0.004 | 0.202 | |