Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 2189/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TSAR 1.5.0 (landing page) Xinlin Gao
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the TSAR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TSAR.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: TSAR |
Version: 1.5.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TSAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TSAR_1.5.0.tar.gz |
StartedAt: 2024-12-24 12:21:10 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 12:24:30 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 199.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TSAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:TSAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TSAR_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TSAR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TSAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TSAR’ 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 ‘TSAR’ 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION Most likely ‘inst/CITATION’ should be used instead. Warning: program compiled against libxml 212 using older 211 * 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 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 ... NOTE TSA_Tms : <anonymous>: no visible binding for global variable ‘well_ID’ TSA_Tms : <anonymous>: no visible binding for global variable ‘Tm’ TSA_Tms : <anonymous>: no visible global function definition for ‘sd’ TSA_Tms: no visible binding for global variable ‘well_ID’ TSA_Tms: no visible binding for global variable ‘Tm’ TSA_Tms: no visible binding for global variable ‘condition_ID’ TSA_Tms: no visible binding for global variable ‘Protein’ TSA_Tms: no visible binding for global variable ‘Ligand’ TSA_average: no visible binding for global variable ‘Temperature’ TSA_average: no visible binding for global variable ‘Fluorescence’ TSA_average: no visible global function definition for ‘sd’ TSA_average: no visible binding for global variable ‘Normalized’ TSA_average: no visible global function definition for ‘predict’ TSA_boxplot: no visible binding for global variable ‘condition_ID’ TSA_boxplot: no visible binding for global variable ‘Tm’ TSA_boxplot: no visible binding for global variable ‘Ligand’ TSA_boxplot: no visible binding for global variable ‘well_ID’ TSA_boxplot: no visible binding for global variable ‘Protein’ TSA_compare_plot: no visible binding for global variable ‘Temperature’ TSA_compare_plot: no visible binding for global variable ‘avg_smooth’ TSA_compare_plot: no visible binding for global variable ‘sd_min_smooth’ TSA_compare_plot: no visible binding for global variable ‘sd_max_smooth’ TSA_compare_plot: no visible global function definition for ‘colorRampPalette’ TSA_wells_plot: no visible binding for global variable ‘Temperature’ TSA_wells_plot: no visible binding for global variable ‘Fluorescence’ TSA_wells_plot: no visible binding for global variable ‘Normalized’ TSA_wells_plot: no visible binding for global variable ‘well_ID’ TSA_wells_plot: no visible binding for global variable ‘sd_min_smooth’ TSA_wells_plot: no visible binding for global variable ‘sd_max_smooth’ TSA_wells_plot: no visible binding for global variable ‘avg_smooth’ TSA_wells_plot: no visible binding for global variable ‘sd_min’ TSA_wells_plot: no visible binding for global variable ‘sd_max’ TSA_wells_plot: no visible binding for global variable ‘average’ build_curves: no visible binding for global variable ‘condition_ID’ build_table: no visible global function definition for ‘head’ build_well: no visible global function definition for ‘head’ dummy_plot: no visible binding for global variable ‘x’ dummy_plot: no visible binding for global variable ‘y’ gam_analysis : process_well: no visible binding for global variable ‘Well.Position’ gam_analysis : process_well: no visible global function definition for ‘all_of’ join_well_info: no visible binding for global variable ‘Col’ join_well_info: no visible binding for global variable ‘pos’ join_well_info: no visible binding for global variable ‘Well’ join_well_info: no visible binding for global variable ‘Protein’ join_well_info: no visible binding for global variable ‘Ligand’ join_well_info: no visible global function definition for ‘na.omit’ merge_norm : <anonymous>: no visible global function definition for ‘read.csv’ merge_norm : <anonymous>: no visible binding for global variable ‘Well.Position’ merge_norm : <anonymous>: no visible binding for global variable ‘Protein’ merge_norm : <anonymous>: no visible binding for global variable ‘Ligand’ merge_norm: no visible binding for global variable ‘tm’ merge_norm: no visible binding for global variable ‘Well.Position’ merge_update: no visible global function definition for ‘na.omit’ model_boltzmann: no visible binding for global variable ‘Temperature’ normalize: no visible global function definition for ‘all_of’ preview_condition: no visible global function definition for ‘head’ preview_model: no visible binding for global variable ‘Well.Position’ read_analysis: no visible global function definition for ‘read.delim’ read_analysis: no visible global function definition for ‘read.csv’ read_raw_data: no visible global function definition for ‘read.delim’ read_raw_data: no visible global function definition for ‘read.csv’ remove_raw: no visible binding for global variable ‘Well.Position’ remove_raw: no visible binding for global variable ‘Well’ remove_selected_graph: no visible binding for global variable ‘condition_ID’ remove_selected_graph: no visible binding for global variable ‘well_ID’ screen: no visible binding for global variable ‘Well.Position’ screen: no visible binding for global variable ‘Well’ screen : normalize_by_well: no visible binding for global variable ‘Well.Position’ screen: no visible binding for global variable ‘Temperature’ screen: no visible binding for global variable ‘Fluorescence’ view_deriv: no visible binding for global variable ‘Temperature’ view_deriv: no visible binding for global variable ‘norm_deriv’ view_deriv: no visible binding for global variable ‘well_ID’ view_deriv: no visible binding for global variable ‘Tm’ view_model: no visible binding for global variable ‘Temperature’ view_model: no visible binding for global variable ‘Normalized’ view_model: no visible binding for global variable ‘fitted’ view_model: no visible global function definition for ‘na.omit’ view_model: no visible binding for global variable ‘norm_deriv’ view_model: no visible binding for global variable ‘Well.Position’ Undefined global functions or variables: Col Fluorescence Ligand Normalized Protein Temperature Tm Well Well.Position all_of average avg_smooth colorRampPalette condition_ID fitted head na.omit norm_deriv pos predict read.csv read.delim sd sd_max sd_max_smooth sd_min sd_min_smooth tm well_ID x y Consider adding importFrom("grDevices", "colorRampPalette") importFrom("stats", "fitted", "na.omit", "predict", "sd") importFrom("utils", "head", "read.csv", "read.delim") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: model_gam.Rd: gam Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TSA_wells_plot 29.733 0.737 38.520 gam_analysis 7.759 0.140 10.679 view_deriv 7.355 0.184 11.892 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/TSAR.Rcheck/00check.log’ for details.
TSAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL TSAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘TSAR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (TSAR)
TSAR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(TSAR) Attaching package: 'TSAR' The following object is masked from 'package:graphics': screen > > test_check("TSAR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 11.749 0.480 15.275
TSAR.Rcheck/TSAR-Ex.timings
name | user | system | elapsed | |
TSA_Tms | 0.234 | 0.000 | 0.255 | |
TSA_boxplot | 1.266 | 0.020 | 1.861 | |
TSA_ligands | 0.203 | 0.000 | 0.407 | |
TSA_proteins | 0.226 | 0.012 | 0.479 | |
TSA_wells_plot | 29.733 | 0.737 | 38.520 | |
Tm_difference | 0.236 | 0.024 | 0.322 | |
Tm_est | 1.168 | 0.028 | 2.253 | |
analyze_norm | 0 | 0 | 0 | |
condition_IDs | 0.224 | 0.000 | 0.448 | |
gam_analysis | 7.759 | 0.140 | 10.679 | |
get_legend | 0.701 | 0.000 | 0.763 | |
graph_tsar | 0 | 0 | 0 | |
join_well_info | 0.859 | 0.116 | 0.982 | |
merge_norm | 1.341 | 0.000 | 1.345 | |
merge_tsa | 0 | 0 | 0 | |
model_boltzmann | 0.106 | 0.000 | 0.106 | |
model_fit | 1.162 | 0.004 | 1.420 | |
model_gam | 1.111 | 0.000 | 1.677 | |
normalize | 0.068 | 0.000 | 0.068 | |
normalize_fluorescence | 0 | 0 | 0 | |
read_analysis | 0 | 0 | 0 | |
read_raw_data | 0 | 0 | 0 | |
read_tsar | 0.603 | 0.004 | 0.620 | |
remove_raw | 0.253 | 0.103 | 0.441 | |
rescale | 0.001 | 0.000 | 0.001 | |
run_boltzmann | 0.086 | 0.000 | 0.087 | |
screen | 0.983 | 0.000 | 1.017 | |
tsa_average | 0.492 | 0.004 | 0.497 | |
tsa_compare_plot | 3.372 | 0.008 | 4.011 | |
view_deriv | 7.355 | 0.184 | 11.892 | |
view_model | 1.662 | 0.000 | 2.091 | |
weed_raw | 0.058 | 0.003 | 0.061 | |
well_IDs | 0.231 | 0.004 | 0.235 | |
write_tsar | 0.595 | 0.000 | 0.656 | |