Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:39:55 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1881/2251 | 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 | ![]() | ||||||||
merida1 | 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: 2024-03-02 10:22:46 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 10:32:20 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 574.8 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) (2024-01-16 r85808) * 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 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 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 ... 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 ... 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 79.811 2.104 103.624 plot_zscore_distribution 75.904 1.962 99.002 compute_metrics 42.878 2.160 53.539 find_robust_zscore_hit 36.925 2.846 46.868 find_zscore_hit 37.641 1.197 46.183 plot_trend 3.401 1.899 6.958 plot_barcode_lost_for_gene 3.914 0.114 5.045 plot_mapped_reads_distribution 3.678 0.176 5.066 * 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: 1 NOTE 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) (2024-01-16 r85808) -- "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 56.047 1.798 71.146
ScreenR.Rcheck/ScreenR-Ex.timings
name | user | system | elapsed | |
barcode_lost | 0.340 | 0.060 | 0.468 | |
compute_data_table | 0.600 | 0.017 | 0.726 | |
compute_explained_variance | 0.043 | 0.006 | 0.060 | |
compute_metrics | 42.878 | 2.160 | 53.539 | |
compute_slope | 0.091 | 0.002 | 0.105 | |
count_mapped_reads | 0.147 | 0.035 | 0.216 | |
create_edger_obj | 0.048 | 0.003 | 0.060 | |
create_screenr_object | 0.091 | 0.003 | 0.108 | |
filter_by_slope | 0.244 | 0.006 | 0.284 | |
filter_by_variance | 2.298 | 0.037 | 2.985 | |
find_camera_hit | 2.450 | 0.055 | 3.279 | |
find_common_hit | 0.064 | 0.001 | 0.091 | |
find_roast_hit | 3.844 | 0.066 | 4.725 | |
find_robust_zscore_hit | 36.925 | 2.846 | 46.868 | |
find_zscore_hit | 37.641 | 1.197 | 46.183 | |
get_annotation_table | 0.035 | 0.001 | 0.043 | |
get_count_table | 0.168 | 0.005 | 0.202 | |
get_data_table | 0.074 | 0.001 | 0.098 | |
get_groups | 0.001 | 0.000 | 0.002 | |
get_normalized_count_table | 0.095 | 0.001 | 0.111 | |
get_replicates | 0 | 0 | 0 | |
mapped_reads | 0.172 | 0.035 | 0.244 | |
normalize_data | 0.107 | 0.001 | 0.124 | |
plot_barcode_hit | 2.160 | 0.018 | 2.852 | |
plot_barcode_lost | 1.617 | 1.672 | 3.898 | |
plot_barcode_lost_for_gene | 3.914 | 0.114 | 5.045 | |
plot_barcode_trend | 79.811 | 2.104 | 103.624 | |
plot_boxplot | 0.825 | 0.010 | 1.081 | |
plot_common_hit | 0.406 | 0.008 | 0.534 | |
plot_explained_variance | 1.494 | 0.022 | 1.972 | |
plot_mapped_reads | 0.598 | 0.040 | 0.827 | |
plot_mapped_reads_distribution | 3.678 | 0.176 | 5.066 | |
plot_mds | 1.076 | 0.011 | 1.425 | |
plot_trend | 3.401 | 1.899 | 6.958 | |
plot_zscore_distribution | 75.904 | 1.962 | 99.002 | |
remove_all_zero_row | 0.022 | 0.001 | 0.034 | |
set_annotation_table | 0.305 | 0.005 | 0.413 | |
set_count_table | 0.296 | 0.005 | 0.398 | |
set_data_table | 0.296 | 0.004 | 0.394 | |
set_groups | 0.303 | 0.005 | 0.425 | |
set_normalized_count_table | 0.392 | 0.006 | 0.535 | |
set_replicates | 0.299 | 0.005 | 0.412 | |