Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1611/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
protGear 1.10.0 (landing page) Kennedy Mwai
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the protGear package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/protGear.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: protGear |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:protGear.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings protGear_1.10.0.tar.gz |
StartedAt: 2024-12-20 04:24:18 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:27:32 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 194.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: protGear.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:protGear.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings protGear_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/protGear.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘protGear/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘protGear’ version ‘1.10.0’ * 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 ‘protGear’ 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 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 best_CV_estimation: no visible binding for global variable ‘x’ best_CV_estimation: no visible binding for global variable ‘prop’ best_CV_estimation: no visible binding for global variable ‘val’ best_CV_estimation: no visible binding for global variable ‘meanX1_X2’ best_CV_estimation: no visible binding for global variable ‘meanX2_X3’ best_CV_estimation: no visible binding for global variable ‘xbar’ best_CV_estimation: no visible binding for global variable ‘CVX’ best_CV_estimation: no visible binding for global variable ‘meanX’ best_CV_estimation: no visible binding for global variable ‘selected’ best_CV_estimation: no visible binding for global variable ‘CVX2_X3’ best_CV_estimation: no visible binding for global variable ‘CVX1_X3’ best_CV_estimation: no visible binding for global variable ‘CVX1_X2’ best_CV_estimation: no visible binding for global variable ‘best_CV’ best_CV_estimation: no visible binding for global variable ‘FMedianBG_correct’ bg_correct: no visible binding for global variable ‘sampleID’ bg_correct: no visible binding for global variable ‘Name’ bg_correct: no visible binding for global variable ‘antigen’ bg_correct: no visible binding for global variable ‘sample_array_ID’ bg_correct: no visible binding for global variable ‘Block’ bg_correct: no visible binding for global variable ‘Column’ bg_correct: no visible binding for global variable ‘Row’ bg_correct: no visible binding for global variable ‘FMedian’ bg_correct: no visible binding for global variable ‘FMedianBG_correct’ bg_correct: no visible binding for global variable ‘global_BGMedian’ bg_correct: no visible binding for global variable ‘minimum_BGMedian’ bg_correct: no visible binding for global variable ‘BGMedian’ buffer_spots: no visible binding for global variable ‘sampleID’ buffer_spots: no visible binding for global variable ‘antigen’ buffer_spots: no visible binding for global variable ‘FMedianBG_correct’ buffer_spots: no visible binding for global variable ‘Block’ buffer_spots: no visible binding for global variable ‘Column’ buffer_spots: no visible binding for global variable ‘Row’ cv_by_sample_estimation: no visible binding for global variable ‘variable’ cv_by_sample_estimation: no visible binding for global variable ‘value’ cv_by_sample_estimation: no visible binding for global variable ‘temp’ cv_estimation: no visible binding for global variable ‘FMedianBG_correct’ cv_estimation: no visible binding for global variable ‘sdX’ cv_estimation: no visible binding for global variable ‘meanX’ cv_estimation: no visible binding for global variable ‘sdX2_X3’ cv_estimation: no visible binding for global variable ‘meanX2_X3’ cv_estimation: no visible binding for global variable ‘sdX1_X3’ cv_estimation: no visible binding for global variable ‘meanX1_X3’ cv_estimation: no visible binding for global variable ‘sdX1_X2’ cv_estimation: no visible binding for global variable ‘meanX1_X2’ cv_estimation: no visible binding for global variable ‘CVX’ cv_estimation: no visible binding for global variable ‘CVX2_X3’ cv_estimation: no visible binding for global variable ‘CVX1_X3’ cv_estimation: no visible binding for global variable ‘CVX1_X2’ cv_estimation: no visible binding for global variable ‘antigen’ cv_estimation: no visible binding for global variable ‘sampleID’ cv_estimation: no visible binding for global variable ‘sample_array_ID’ extract_bg: no visible binding for global variable ‘v1’ extract_bg: no visible binding for global variable ‘v2’ extract_bg: no visible binding for global variable ‘index’ extract_bg: no visible binding for global variable ‘Name’ extract_bg: no visible binding for global variable ‘Block’ extract_bg: no visible binding for global variable ‘antigen’ matrix_normalise: no visible binding for global variable ‘day_batches’ matrix_normalise: no visible binding for global variable ‘machines’ matrix_normalise: no visible binding for global variable ‘variable’ matrix_normalise: no visible binding for global variable ‘value’ matrix_normalise: no visible binding for global variable ‘antigen’ matrix_normalise: no visible binding for global variable ‘sampleID2’ matrix_normalise: no visible binding for global variable ‘temp’ merge_sampleID: no visible binding for global variable ‘v1’ merge_sampleID: no visible binding for global variable ‘v2’ merge_sampleID: no visible binding for global variable ‘index’ merge_sampleID: no visible binding for global variable ‘Name’ plot_FB: no visible binding for global variable ‘.id’ plot_FB: no visible binding for global variable ‘log_fb’ plot_FB: no visible binding for global variable ‘log_bg’ plot_FB: no visible binding for global variable ‘antigen’ plot_FB: no visible binding for global variable ‘FBG_Median’ plot_FB: no visible binding for global variable ‘BG_Median’ plot_bg: no visible binding for global variable ‘.id’ plot_buffer: no visible binding for global variable ‘buffers’ plot_normalised: no visible binding for global variable ‘mean_all_anti’ plot_normalised: no visible binding for global variable ‘rank_mean_all_anti’ plot_normalised: no visible binding for global variable ‘stdev_all_anti’ plot_normalised_antigen: no visible binding for global variable ‘antigen’ plot_normalised_antigen: no visible binding for global variable ‘MFI’ plot_normalised_antigen: no visible binding for global variable ‘mean_mfi’ plot_normalised_antigen: no visible binding for global variable ‘rank_mean_all_anti’ plot_normalised_antigen: no visible binding for global variable ‘sd_mfi’ read_array_files: no visible binding for global variable ‘Block’ read_array_files: no visible binding for global variable ‘global_BGMedian’ read_array_files: no visible binding for global variable ‘minimum_BGMedian’ rlm_normalise: no visible binding for global variable ‘Description’ rlm_normalise: no visible binding for global variable ‘Array’ rlm_normalise: no visible binding for global variable ‘Block’ rlm_normalise: no visible binding for global variable ‘antigen’ rlm_normalise: no visible binding for global variable ‘MFI_val’ rlm_normalise: no visible binding for global variable ‘antigen_name’ rlm_normalise: no visible binding for global variable ‘meanBest2_RLM’ rlm_normalise: no visible binding for global variable ‘sample_index’ rlm_normalise: no visible binding for global variable ‘slide’ rlm_normalise: no visible binding for global variable ‘sampleID2’ rlm_normalise_matrix: no visible binding for global variable ‘slide’ rlm_normalise_matrix: no visible binding for global variable ‘sample_index’ rlm_normalise_matrix: no visible binding for global variable ‘antigen’ rlm_normalise_matrix: no visible binding for global variable ‘MFI_val’ rlm_normalise_matrix: no visible binding for global variable ‘sample_array_ID’ rlm_normalise_matrix: no visible binding for global variable ‘Block’ tag_subtract: no visible binding for global variable ‘TAG’ tag_subtract: no visible binding for global variable ‘TAG_name’ tag_subtract: no visible binding for global variable ‘TAG_mfi’ visualize_slide: no visible binding for global variable ‘Block’ visualize_slide: no visible binding for global variable ‘X’ visualize_slide: no visible binding for global variable ‘Y’ visualize_slide: no visible binding for global variable ‘meanX’ visualize_slide: no visible binding for global variable ‘meanY’ visualize_slide_2d: no visible binding for global variable ‘Block’ visualize_slide_2d: no visible binding for global variable ‘X’ visualize_slide_2d: no visible binding for global variable ‘Y’ visualize_slide_2d: no visible binding for global variable ‘meanX’ visualize_slide_2d: no visible binding for global variable ‘meanY’ Undefined global functions or variables: .id Array BGMedian BG_Median Block CVX CVX1_X2 CVX1_X3 CVX2_X3 Column Description FBG_Median FMedian FMedianBG_correct MFI MFI_val Name Row TAG TAG_mfi TAG_name X Y antigen antigen_name best_CV buffers day_batches global_BGMedian index log_bg log_fb machines meanBest2_RLM meanX meanX1_X2 meanX1_X3 meanX2_X3 meanY mean_all_anti mean_mfi minimum_BGMedian prop rank_mean_all_anti sampleID sampleID2 sample_array_ID sample_index sdX sdX1_X2 sdX1_X3 sdX2_X3 sd_mfi selected slide stdev_all_anti temp v1 v2 val value variable x xbar * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/protGear.Rcheck/00check.log’ for details.
protGear.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL protGear ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘protGear’ ... ** using staged installation ** R ** 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 (protGear)
protGear.Rcheck/protGear-Ex.timings
name | user | system | elapsed | |
array_vars | 0.001 | 0.000 | 0.001 | |
best_CV_estimation | 0.431 | 0.065 | 0.491 | |
buffer_spots | 0.077 | 0.026 | 0.101 | |
check_sampleID_files | 0.002 | 0.001 | 0.003 | |
create_dir | 0 | 0 | 0 | |
cv_by_sample_estimation | 0.151 | 0.036 | 0.187 | |
cv_estimation | 0.142 | 0.044 | 0.186 | |
extract_bg | 0.272 | 0.034 | 0.306 | |
launch_protGear_interactive | 0.001 | 0.000 | 0.002 | |
launch_select | 0.001 | 0.000 | 0.002 | |
matrix_normalise | 0.921 | 0.700 | 1.608 | |
merge_sampleID | 0.322 | 0.026 | 0.348 | |
minpositive | 0 | 0 | 0 | |
name_of_files | 0 | 0 | 0 | |
output_trend_stats | 0.000 | 0.000 | 0.001 | |
plot_FB | 0.267 | 0.105 | 0.371 | |
plot_bg | 1.073 | 0.229 | 1.301 | |
plot_buffer | 0.433 | 0.026 | 0.457 | |
plot_normalised | 0.896 | 0.420 | 1.324 | |
plot_normalised_antigen | 0.818 | 0.376 | 1.204 | |
read_array_files | 0.064 | 0.003 | 0.068 | |
read_array_visualize | 0.029 | 0.008 | 0.038 | |
rlm_normalise | 0.025 | 0.359 | 0.394 | |
rlm_normalise_matrix | 0.052 | 0.372 | 0.432 | |
tag_subtract | 0.269 | 0.050 | 0.318 | |
visualize_slide | 0.683 | 0.029 | 0.712 | |
visualize_slide_2d | 0.337 | 0.010 | 0.347 | |