| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1859/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.2.0 (landing page) Emanuel Michele Soda
| kjohnson2 | macOS 12.6.1 Monterey / 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: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2023-10-18 23:11:57 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 23:20:35 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 517.1 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ScreenR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.2.0’
* 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_zscore_distribution 49.580 6.277 100.807
plot_barcode_trend 45.545 4.131 88.117
compute_metrics 25.947 1.305 49.008
find_zscore_hit 22.472 2.548 45.014
find_robust_zscore_hit 22.653 2.030 44.217
plot_mapped_reads_distribution 2.480 0.736 5.581
* 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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
30.264 0.819 55.975
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.194 | 0.020 | 0.377 | |
| compute_data_table | 0.316 | 0.010 | 0.581 | |
| compute_explained_variance | 0.030 | 0.002 | 0.058 | |
| compute_metrics | 25.947 | 1.305 | 49.008 | |
| compute_slope | 0.064 | 0.004 | 0.113 | |
| count_mapped_reads | 0.062 | 0.010 | 0.133 | |
| create_edger_obj | 0.032 | 0.002 | 0.058 | |
| create_screenr_object | 0.063 | 0.002 | 0.115 | |
| filter_by_slope | 0.167 | 0.007 | 0.319 | |
| filter_by_variance | 1.483 | 0.029 | 2.740 | |
| find_camera_hit | 1.563 | 0.041 | 2.900 | |
| find_common_hit | 0.042 | 0.001 | 0.076 | |
| find_roast_hit | 2.332 | 0.053 | 4.307 | |
| find_robust_zscore_hit | 22.653 | 2.030 | 44.217 | |
| find_zscore_hit | 22.472 | 2.548 | 45.014 | |
| get_annotation_table | 0.017 | 0.001 | 0.028 | |
| get_count_table | 0.104 | 0.014 | 0.196 | |
| get_data_table | 0.035 | 0.001 | 0.067 | |
| get_groups | 0.001 | 0.000 | 0.001 | |
| get_normalized_count_table | 0.056 | 0.001 | 0.099 | |
| get_replicates | 0.001 | 0.000 | 0.004 | |
| mapped_reads | 0.088 | 0.010 | 0.178 | |
| normalize_data | 0.057 | 0.001 | 0.103 | |
| plot_barcode_hit | 1.453 | 0.063 | 2.700 | |
| plot_barcode_lost | 0.417 | 0.029 | 0.782 | |
| plot_barcode_lost_for_gene | 1.533 | 0.038 | 2.781 | |
| plot_barcode_trend | 45.545 | 4.131 | 88.117 | |
| plot_boxplot | 0.428 | 0.008 | 0.784 | |
| plot_common_hit | 0.210 | 0.008 | 0.379 | |
| plot_explained_variance | 0.436 | 0.007 | 0.793 | |
| plot_mapped_reads | 0.226 | 0.012 | 0.430 | |
| plot_mapped_reads_distribution | 2.480 | 0.736 | 5.581 | |
| plot_mds | 0.439 | 0.013 | 0.807 | |
| plot_trend | 1.687 | 0.070 | 3.133 | |
| plot_zscore_distribution | 49.580 | 6.277 | 100.807 | |
| remove_all_zero_row | 0.014 | 0.001 | 0.027 | |
| set_annotation_table | 0.161 | 0.003 | 0.290 | |
| set_count_table | 0.154 | 0.002 | 0.280 | |
| set_data_table | 0.159 | 0.002 | 0.293 | |
| set_groups | 0.171 | 0.002 | 0.315 | |
| set_normalized_count_table | 0.219 | 0.003 | 0.398 | |
| set_replicates | 0.155 | 0.002 | 0.282 | |