Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1863/2239 | 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 | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ScreenR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ScreenR_1.7.0.tar.gz |
StartedAt: 2024-06-10 09:20:16 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 09:29:13 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 536.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ScreenR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ScreenR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ScreenR_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ScreenR.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ScreenR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ScreenR' version '1.7.0' * 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 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 47.83 4.49 52.22 plot_zscore_distribution 45.38 4.33 49.59 compute_metrics 27.42 1.13 28.55 find_robust_zscore_hit 22.03 3.00 24.99 find_zscore_hit 21.41 1.31 22.68 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/ScreenR.Rcheck/00check.log' for details.
ScreenR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 29.87 11.28 41.26
ScreenR.Rcheck/ScreenR-Ex.timings
name | user | system | elapsed | |
barcode_lost | 0.09 | 0.05 | 0.14 | |
compute_data_table | 0.24 | 0.00 | 0.24 | |
compute_explained_variance | 0.02 | 0.00 | 0.02 | |
compute_metrics | 27.42 | 1.13 | 28.55 | |
compute_slope | 0.06 | 0.00 | 0.06 | |
count_mapped_reads | 0.02 | 0.01 | 0.03 | |
create_edger_obj | 0.03 | 0.02 | 0.03 | |
create_screenr_object | 0.03 | 0.00 | 0.03 | |
filter_by_slope | 0.14 | 0.02 | 0.16 | |
filter_by_variance | 1.78 | 0.10 | 1.89 | |
find_camera_hit | 1.82 | 0.05 | 1.86 | |
find_common_hit | 0.04 | 0.00 | 0.05 | |
find_roast_hit | 2.50 | 0.02 | 2.51 | |
find_robust_zscore_hit | 22.03 | 3.00 | 24.99 | |
find_zscore_hit | 21.41 | 1.31 | 22.68 | |
get_annotation_table | 0.02 | 0.00 | 0.02 | |
get_count_table | 0.07 | 0.12 | 0.20 | |
get_data_table | 0.03 | 0.02 | 0.03 | |
get_groups | 0 | 0 | 0 | |
get_normalized_count_table | 0.05 | 0.00 | 0.05 | |
get_replicates | 0 | 0 | 0 | |
mapped_reads | 0.08 | 0.00 | 0.08 | |
normalize_data | 0.06 | 0.00 | 0.06 | |
plot_barcode_hit | 1.36 | 0.11 | 1.47 | |
plot_barcode_lost | 0.66 | 0.25 | 0.92 | |
plot_barcode_lost_for_gene | 1.26 | 0.03 | 1.28 | |
plot_barcode_trend | 47.83 | 4.49 | 52.22 | |
plot_boxplot | 0.29 | 0.01 | 0.31 | |
plot_common_hit | 0.19 | 0.00 | 0.20 | |
plot_explained_variance | 0.39 | 0.00 | 0.39 | |
plot_mapped_reads | 0.21 | 0.00 | 0.21 | |
plot_mapped_reads_distribution | 1.39 | 0.02 | 1.40 | |
plot_mds | 0.43 | 0.01 | 0.46 | |
plot_trend | 1.69 | 0.56 | 2.25 | |
plot_zscore_distribution | 45.38 | 4.33 | 49.59 | |
remove_all_zero_row | 0.01 | 0.00 | 0.02 | |
set_annotation_table | 0.16 | 0.00 | 0.15 | |
set_count_table | 0.11 | 0.00 | 0.11 | |
set_data_table | 0.12 | 0.00 | 0.13 | |
set_groups | 0.13 | 0.00 | 0.12 | |
set_normalized_count_table | 0.15 | 0.00 | 0.16 | |
set_replicates | 0.11 | 0.00 | 0.11 | |