Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:40:01 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1894/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ScreenR 1.5.0 (landing page) Emanuel Michele Soda
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.5.0 |
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_1.5.0.tar.gz |
StartedAt: 2024-03-27 23:59:21 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-28 00:04:09 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 288.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ScreenR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ScreenR.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-apple-darwin20 * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ScreenR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ScreenR’ version ‘1.5.0’ * 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 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_barcode_trend 44.541 3.449 48.461 plot_zscore_distribution 42.670 5.074 48.297 compute_metrics 24.101 2.900 27.253 find_zscore_hit 20.606 2.466 23.327 find_robust_zscore_hit 19.046 1.116 20.317 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ScreenR.Rcheck/00check.log’ for details.
ScreenR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 30.978 1.388 32.749
ScreenR.Rcheck/ScreenR-Ex.timings
name | user | system | elapsed | |
barcode_lost | 0.230 | 0.044 | 0.275 | |
compute_data_table | 0.305 | 0.013 | 0.324 | |
compute_explained_variance | 0.025 | 0.004 | 0.029 | |
compute_metrics | 24.101 | 2.900 | 27.253 | |
compute_slope | 0.049 | 0.000 | 0.051 | |
count_mapped_reads | 0.091 | 0.050 | 0.147 | |
create_edger_obj | 0.023 | 0.001 | 0.024 | |
create_screenr_object | 0.053 | 0.001 | 0.055 | |
filter_by_slope | 0.134 | 0.003 | 0.139 | |
filter_by_variance | 1.265 | 0.164 | 1.438 | |
find_camera_hit | 1.360 | 0.152 | 1.525 | |
find_common_hit | 0.033 | 0.000 | 0.034 | |
find_roast_hit | 1.973 | 0.214 | 2.210 | |
find_robust_zscore_hit | 19.046 | 1.116 | 20.317 | |
find_zscore_hit | 20.606 | 2.466 | 23.327 | |
get_annotation_table | 0.018 | 0.001 | 0.019 | |
get_count_table | 0.108 | 0.015 | 0.123 | |
get_data_table | 0.035 | 0.001 | 0.035 | |
get_groups | 0.000 | 0.000 | 0.001 | |
get_normalized_count_table | 0.051 | 0.000 | 0.052 | |
get_replicates | 0 | 0 | 0 | |
mapped_reads | 0.118 | 0.045 | 0.206 | |
normalize_data | 0.057 | 0.001 | 0.061 | |
plot_barcode_hit | 1.288 | 0.017 | 1.316 | |
plot_barcode_lost | 0.892 | 0.328 | 1.239 | |
plot_barcode_lost_for_gene | 1.878 | 0.060 | 1.989 | |
plot_barcode_trend | 44.541 | 3.449 | 48.461 | |
plot_boxplot | 0.455 | 0.006 | 0.464 | |
plot_common_hit | 0.233 | 0.006 | 0.243 | |
plot_explained_variance | 0.901 | 0.016 | 0.930 | |
plot_mapped_reads | 0.351 | 0.030 | 0.384 | |
plot_mapped_reads_distribution | 2.117 | 0.148 | 2.313 | |
plot_mds | 0.808 | 2.246 | 3.180 | |
plot_trend | 1.978 | 0.180 | 2.187 | |
plot_zscore_distribution | 42.670 | 5.074 | 48.297 | |
remove_all_zero_row | 0.012 | 0.001 | 0.012 | |
set_annotation_table | 0.161 | 0.002 | 0.164 | |
set_count_table | 0.149 | 0.010 | 0.159 | |
set_data_table | 0.138 | 0.001 | 0.141 | |
set_groups | 0.152 | 0.003 | 0.156 | |
set_normalized_count_table | 0.211 | 0.003 | 0.215 | |
set_replicates | 0.142 | 0.001 | 0.145 | |