Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:29 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1562/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
protGear 1.3.32 (landing page) Kennedy Mwai
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: protGear |
Version: 1.3.32 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:protGear.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings protGear_1.3.32.tar.gz |
StartedAt: 2023-04-11 22:41:19 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 22:45:05 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 225.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: protGear.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:protGear.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings protGear_1.3.32.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/protGear.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘protGear/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘protGear’ version ‘1.3.32’ * 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 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 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/protGear.Rcheck/00check.log’ for details.
protGear.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL protGear ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 | 0.504 | 0.083 | 0.600 | |
buffer_spots | 0.084 | 0.024 | 0.098 | |
check_sampleID_files | 0.001 | 0.002 | 0.004 | |
create_dir | 0 | 0 | 0 | |
cv_by_sample_estimation | 0.221 | 0.016 | 0.227 | |
cv_estimation | 0.172 | 0.036 | 0.197 | |
extract_bg | 0.262 | 0.016 | 0.280 | |
launch_protGear_interactive | 0.002 | 0.000 | 0.002 | |
launch_select | 0.002 | 0.000 | 0.001 | |
matrix_normalise | 1.387 | 0.313 | 1.566 | |
merge_sampleID | 0.32 | 0.00 | 0.32 | |
minpositive | 0 | 0 | 0 | |
name_of_files | 0.001 | 0.000 | 0.001 | |
output_trend_stats | 0 | 0 | 0 | |
plot_FB | 0.240 | 0.021 | 0.255 | |
plot_bg | 0.450 | 0.019 | 0.465 | |
plot_buffer | 1.141 | 0.052 | 1.189 | |
plot_normalised | 1.234 | 0.364 | 1.474 | |
plot_normalised_antigen | 1.256 | 0.361 | 1.488 | |
read_array_files | 0.059 | 0.003 | 0.063 | |
read_array_visualize | 0.032 | 0.000 | 0.032 | |
rlm_normalise | 0.139 | 0.343 | 0.345 | |
rlm_normalise_matrix | 0.122 | 0.327 | 0.310 | |
tag_subtract | 0.320 | 0.036 | 0.346 | |
visualize_slide | 0.714 | 0.008 | 0.722 | |
visualize_slide_2d | 0.366 | 0.024 | 0.390 | |