| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:51 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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: - 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 1819/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.0.0 (landing page) Emanuel Michele Soda
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ScreenR |
| Version: 1.0.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ScreenR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ScreenR_1.0.0.tar.gz |
| StartedAt: 2023-04-11 05:48:23 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 06:05:46 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 1043.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScreenR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ScreenR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ScreenR_1.0.0.tar.gz
###
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##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/ScreenR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ScreenR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ScreenR' version '1.0.0'
* 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 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_barcode_trend 242.41 8.05 251.17
plot_zscore_distribution 222.45 8.13 230.75
find_zscore_hit 202.92 3.40 206.39
find_robust_zscore_hit 167.97 4.11 172.08
compute_metrics 59.86 2.24 62.11
find_roast_hit 5.87 0.13 6.00
find_camera_hit 5.17 0.03 5.20
* 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: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-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 version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
26.29 1.78 28.15
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.18 | 0.00 | 0.19 | |
| compute_data_table | 0.27 | 0.00 | 0.26 | |
| compute_explained_variance | 0.02 | 0.00 | 0.01 | |
| compute_metrics | 59.86 | 2.24 | 62.11 | |
| compute_slope | 0.09 | 0.00 | 0.10 | |
| count_mapped_reads | 0.10 | 0.01 | 0.11 | |
| create_edger_obj | 0.09 | 0.00 | 0.09 | |
| create_screenr_object | 0.06 | 0.00 | 0.06 | |
| filter_by_slope | 0.34 | 0.02 | 0.36 | |
| filter_by_variance | 3.49 | 0.00 | 3.48 | |
| find_camera_hit | 5.17 | 0.03 | 5.20 | |
| find_common_hit | 1.08 | 0.00 | 1.08 | |
| find_roast_hit | 5.87 | 0.13 | 6.00 | |
| find_robust_zscore_hit | 167.97 | 4.11 | 172.08 | |
| find_zscore_hit | 202.92 | 3.40 | 206.39 | |
| get_annotation_table | 0 | 0 | 0 | |
| get_count_table | 0.06 | 0.14 | 0.22 | |
| get_data_table | 0.04 | 0.00 | 0.04 | |
| get_groups | 0 | 0 | 0 | |
| get_normalized_count_table | 0.07 | 0.00 | 0.07 | |
| get_replicates | 0 | 0 | 0 | |
| mapped_reads | 0.06 | 0.00 | 0.06 | |
| normalize_data | 0.06 | 0.00 | 0.06 | |
| plot_barcode_hit | 1.59 | 0.17 | 1.77 | |
| plot_barcode_lost | 0.41 | 0.09 | 0.50 | |
| plot_barcode_lost_for_gene | 1.34 | 0.00 | 1.34 | |
| plot_barcode_trend | 242.41 | 8.05 | 251.17 | |
| plot_boxplot | 0.58 | 0.03 | 0.63 | |
| plot_common_hit | 0.30 | 0.00 | 1.61 | |
| plot_explained_variance | 0.59 | 0.02 | 0.61 | |
| plot_mapped_reads | 0.33 | 0.00 | 0.32 | |
| plot_mapped_reads_distribution | 3.31 | 0.06 | 3.40 | |
| plot_mds | 0.92 | 0.02 | 0.93 | |
| plot_trend | 2.22 | 0.07 | 2.80 | |
| plot_zscore_distribution | 222.45 | 8.13 | 230.75 | |
| remove_all_zero_row | 0.03 | 0.00 | 0.03 | |
| set_annotation_table | 0.29 | 0.00 | 0.28 | |
| set_count_table | 0.12 | 0.00 | 0.13 | |
| set_data_table | 0.14 | 0.00 | 0.14 | |
| set_groups | 0.97 | 0.01 | 0.98 | |
| set_normalized_count_table | 0.19 | 0.00 | 0.19 | |
| set_replicates | 0.15 | 0.00 | 0.16 | |