| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:18 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 | ||||
| Package 1896/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.4.0 (landing page) Emanuel Michele Soda
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the ScreenR package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ScreenR |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ScreenR_1.4.0.tar.gz |
| StartedAt: 2024-04-18 03:11:47 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 03:16:24 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 276.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScreenR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ScreenR_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ScreenR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.4.0’
* 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 43.953 3.997 49.004
plot_zscore_distribution 43.162 4.570 49.114
compute_metrics 23.757 1.409 25.765
find_robust_zscore_hit 20.845 2.707 23.993
find_zscore_hit 20.891 1.822 23.134
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
ScreenR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
28.016 1.083 29.520
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.234 | 0.027 | 0.264 | |
| compute_data_table | 0.305 | 0.008 | 0.317 | |
| compute_explained_variance | 0.040 | 0.004 | 0.045 | |
| compute_metrics | 23.757 | 1.409 | 25.765 | |
| compute_slope | 0.051 | 0.001 | 0.052 | |
| count_mapped_reads | 0.055 | 0.010 | 0.066 | |
| create_edger_obj | 0.024 | 0.001 | 0.025 | |
| create_screenr_object | 0.033 | 0.001 | 0.034 | |
| filter_by_slope | 0.130 | 0.004 | 0.137 | |
| filter_by_variance | 1.346 | 0.026 | 1.379 | |
| find_camera_hit | 1.448 | 0.044 | 1.505 | |
| find_common_hit | 0.029 | 0.001 | 0.029 | |
| find_roast_hit | 2.017 | 0.062 | 2.132 | |
| find_robust_zscore_hit | 20.845 | 2.707 | 23.993 | |
| find_zscore_hit | 20.891 | 1.822 | 23.134 | |
| get_annotation_table | 0.014 | 0.000 | 0.014 | |
| get_count_table | 0.108 | 0.007 | 0.115 | |
| get_data_table | 0.027 | 0.001 | 0.028 | |
| get_groups | 0 | 0 | 0 | |
| get_normalized_count_table | 0.034 | 0.000 | 0.035 | |
| get_replicates | 0.000 | 0.000 | 0.001 | |
| mapped_reads | 0.077 | 0.015 | 0.093 | |
| normalize_data | 0.048 | 0.001 | 0.050 | |
| plot_barcode_hit | 1.630 | 0.038 | 1.683 | |
| plot_barcode_lost | 0.757 | 0.048 | 0.852 | |
| plot_barcode_lost_for_gene | 1.277 | 0.014 | 1.374 | |
| plot_barcode_trend | 43.953 | 3.997 | 49.004 | |
| plot_boxplot | 0.391 | 0.004 | 0.409 | |
| plot_common_hit | 0.190 | 0.004 | 0.195 | |
| plot_explained_variance | 0.775 | 0.014 | 0.793 | |
| plot_mapped_reads | 0.293 | 0.021 | 0.344 | |
| plot_mapped_reads_distribution | 1.877 | 0.078 | 1.992 | |
| plot_mds | 0.558 | 0.006 | 0.575 | |
| plot_trend | 2.042 | 0.855 | 2.971 | |
| plot_zscore_distribution | 43.162 | 4.570 | 49.114 | |
| remove_all_zero_row | 0.014 | 0.001 | 0.014 | |
| set_annotation_table | 0.140 | 0.002 | 0.144 | |
| set_count_table | 0.121 | 0.001 | 0.123 | |
| set_data_table | 0.119 | 0.001 | 0.121 | |
| set_groups | 0.127 | 0.002 | 0.129 | |
| set_normalized_count_table | 0.168 | 0.002 | 0.172 | |
| set_replicates | 0.114 | 0.001 | 0.116 | |