Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-23 11:39 -0400 (Tue, 23 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4280 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 1871/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ScreenR 1.7.0 (landing page) Emanuel Michele Soda
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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. - 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: 1.7.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ScreenR_1.7.0.tar.gz |
StartedAt: 2024-07-23 04:08:55 -0400 (Tue, 23 Jul 2024) |
EndedAt: 2024-07-23 04:12:38 -0400 (Tue, 23 Jul 2024) |
EllapsedTime: 223.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ScreenR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ScreenR_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ScreenR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ScreenR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ScreenR’ version ‘1.7.0’ * 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 code 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 loading without being on the library search path ... OK * checking whether 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 ... NOTE checkRd: (-1) annotation_table.Rd:25: Lost braces 25 | \url{https://cellecta.com/}{cellecta}} | ^ * 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 ... NOTE Documented arguments not in \usage in Rd file 'compute_camera.Rd': ‘...’ Documented arguments not in \usage in Rd file 'select_number_barcode.Rd': ‘...’ Documented arguments not in \usage in Rd file 'unique_gene_symbols.Rd': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 40.837 0.408 41.246 plot_barcode_trend 39.316 0.556 39.871 compute_metrics 22.687 1.504 24.191 find_zscore_hit 19.664 0.264 19.928 find_robust_zscore_hit 19.338 0.368 19.706 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/ScreenR.Rcheck/00check.log’ for details.
ScreenR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 22.972 0.517 23.473
ScreenR.Rcheck/ScreenR-Ex.timings
name | user | system | elapsed | |
barcode_lost | 0.135 | 0.012 | 0.146 | |
compute_data_table | 0.197 | 0.000 | 0.197 | |
compute_explained_variance | 0.018 | 0.000 | 0.018 | |
compute_metrics | 22.687 | 1.504 | 24.191 | |
compute_slope | 0.041 | 0.000 | 0.041 | |
count_mapped_reads | 0.033 | 0.000 | 0.033 | |
create_edger_obj | 0.014 | 0.004 | 0.018 | |
create_screenr_object | 0.04 | 0.00 | 0.04 | |
filter_by_slope | 0.114 | 0.000 | 0.114 | |
filter_by_variance | 1.095 | 0.004 | 1.098 | |
find_camera_hit | 1.148 | 0.008 | 1.156 | |
find_common_hit | 0.026 | 0.000 | 0.026 | |
find_roast_hit | 1.715 | 0.008 | 1.722 | |
find_robust_zscore_hit | 19.338 | 0.368 | 19.706 | |
find_zscore_hit | 19.664 | 0.264 | 19.928 | |
get_annotation_table | 0.014 | 0.000 | 0.013 | |
get_count_table | 0.076 | 0.000 | 0.076 | |
get_data_table | 0.026 | 0.000 | 0.026 | |
get_groups | 0.001 | 0.000 | 0.000 | |
get_normalized_count_table | 0.038 | 0.000 | 0.039 | |
get_replicates | 0 | 0 | 0 | |
mapped_reads | 0.052 | 0.000 | 0.052 | |
normalize_data | 0.039 | 0.000 | 0.040 | |
plot_barcode_hit | 1.212 | 0.012 | 1.224 | |
plot_barcode_lost | 0.381 | 0.004 | 0.387 | |
plot_barcode_lost_for_gene | 1.248 | 0.004 | 1.252 | |
plot_barcode_trend | 39.316 | 0.556 | 39.871 | |
plot_boxplot | 0.317 | 0.000 | 0.316 | |
plot_common_hit | 0.182 | 0.004 | 0.186 | |
plot_explained_variance | 0.339 | 0.000 | 0.339 | |
plot_mapped_reads | 0.153 | 0.000 | 0.153 | |
plot_mapped_reads_distribution | 1.458 | 0.008 | 1.466 | |
plot_mds | 0.388 | 0.000 | 0.388 | |
plot_trend | 1.452 | 0.008 | 1.460 | |
plot_zscore_distribution | 40.837 | 0.408 | 41.246 | |
remove_all_zero_row | 0.013 | 0.000 | 0.013 | |
set_annotation_table | 0.132 | 0.004 | 0.135 | |
set_count_table | 0.125 | 0.000 | 0.125 | |
set_data_table | 0.127 | 0.000 | 0.127 | |
set_groups | 0.141 | 0.000 | 0.141 | |
set_normalized_count_table | 0.164 | 0.000 | 0.164 | |
set_replicates | 0.128 | 0.000 | 0.128 | |