Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:29 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R 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

CHECK results for protGear on nebbiolo1


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.

raw results

Package 1562/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
protGear 1.3.32  (landing page)
Kennedy Mwai
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/protGear
git_branch: devel
git_last_commit: ff531ac
git_last_commit_date: 2023-02-03 14:23:38 -0400 (Fri, 03 Feb 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.



Installation output

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)

Tests output


Example timings

protGear.Rcheck/protGear-Ex.timings

nameusersystemelapsed
array_vars0.0010.0000.001
best_CV_estimation0.5040.0830.600
buffer_spots0.0840.0240.098
check_sampleID_files0.0010.0020.004
create_dir000
cv_by_sample_estimation0.2210.0160.227
cv_estimation0.1720.0360.197
extract_bg0.2620.0160.280
launch_protGear_interactive0.0020.0000.002
launch_select0.0020.0000.001
matrix_normalise1.3870.3131.566
merge_sampleID0.320.000.32
minpositive000
name_of_files0.0010.0000.001
output_trend_stats000
plot_FB0.2400.0210.255
plot_bg0.4500.0190.465
plot_buffer1.1410.0521.189
plot_normalised1.2340.3641.474
plot_normalised_antigen1.2560.3611.488
read_array_files0.0590.0030.063
read_array_visualize0.0320.0000.032
rlm_normalise0.1390.3430.345
rlm_normalise_matrix0.1220.3270.310
tag_subtract0.3200.0360.346
visualize_slide0.7140.0080.722
visualize_slide_2d0.3660.0240.390