Kennedy Mwai
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/protGear |
| git_branch: RELEASE_3_20 |
| git_last_commit: 7290eaf |
| git_last_commit_date: 2024-10-29 11:10:05 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:05 -0500 (Thu, 02 Jan 2025).
| 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:protGear.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings protGear_1.10.0.tar.gz |
| StartedAt: 2024-12-31 04:41:45 -0500 (Tue, 31 Dec 2024) |
| EndedAt: 2024-12-31 04:45:22 -0500 (Tue, 31 Dec 2024) |
| EllapsedTime: 216.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: protGear.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:protGear.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings protGear_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/protGear.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.20-bioc/meat/protGear.Rcheck/00check.log'
for details.
protGear.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL protGear ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 | 0 | 0 | |
| best_CV_estimation | 0.62 | 0.14 | 0.76 | |
| buffer_spots | 0.20 | 0.08 | 0.25 | |
| check_sampleID_files | 0.02 | 0.00 | 0.01 | |
| create_dir | 0 | 0 | 0 | |
| cv_by_sample_estimation | 0.28 | 0.08 | 0.35 | |
| cv_estimation | 0.31 | 0.06 | 0.36 | |
| extract_bg | 0.31 | 0.03 | 0.36 | |
| launch_protGear_interactive | 0 | 0 | 0 | |
| launch_select | 0 | 0 | 0 | |
| matrix_normalise | 2.67 | 0.47 | 2.88 | |
| merge_sampleID | 0.39 | 0.00 | 0.39 | |
| minpositive | 0 | 0 | 0 | |
| name_of_files | 0 | 0 | 0 | |
| output_trend_stats | 0 | 0 | 0 | |
| plot_FB | 0.28 | 0.08 | 0.34 | |
| plot_bg | 1.44 | 0.05 | 1.50 | |
| plot_buffer | 0.63 | 0.06 | 0.69 | |
| plot_normalised | 2.64 | 0.66 | 2.89 | |
| plot_normalised_antigen | 2.86 | 0.64 | 2.97 | |
| read_array_files | 0.06 | 0.00 | 0.06 | |
| read_array_visualize | 0.05 | 0.00 | 0.05 | |
| rlm_normalise | 1.06 | 0.45 | 1.26 | |
| rlm_normalise_matrix | 1.12 | 0.52 | 1.22 | |
| tag_subtract | 0.43 | 0.09 | 0.49 | |
| visualize_slide | 0.87 | 0.05 | 0.92 | |
| visualize_slide_2d | 0.42 | 0.01 | 0.44 | |