===============================
R CMD BUILD
===============================
* checking for file ‘protGear/DESCRIPTION’ ... OK
* preparing ‘protGear’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: limma
Loading required package: magrittr
Attaching package: 'magrittr'
The following object is masked from 'package:rlang':
set_names
The following object is masked from 'package:purrr':
set_names
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:magrittr':
extract
Loading required package: tibble
Loading required package: rmarkdown
Loading required package: vsn
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object is masked from 'package:limma':
plotMA
The following object is masked from 'package:gridExtra':
combine
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:rlang':
exprs
Loading required package: genefilter
Loading required package: readr
Attaching package: 'readr'
The following object is masked from 'package:genefilter':
spec
The following object is masked from 'package:scales':
col_factor
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:purrr':
compact
The following object is masked from 'package:ggpubr':
mutate
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:plyr':
arrange, count, desc, failwith, id, mutate, rename, summarise,
summarize
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:gridExtra':
combine
The following object is masked from 'package:kableExtra':
group_rows
The following objects are masked from 'package:data.table':
between, first, last
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Warning: replacing previous import 'magrittr::set_names' by 'rlang::set_names' when loading 'protGear'
Warning: replacing previous import 'gtools::chr' by 'rlang::chr' when loading 'protGear'
Warning: replacing previous import 'dplyr::filter' by 'stats::filter' when loading 'protGear'
Warning: replacing previous import 'dplyr::lag' by 'stats::lag' when loading 'protGear'
Warning: replacing previous import 'magrittr::extract' by 'tidyr::extract' when loading 'protGear'
Warning: replacing previous import 'stats::filter' by 'dplyr::filter' when loading 'protGear'
Warning: replacing previous import 'stats::lag' by 'dplyr::lag' when loading 'protGear'
Warning: replacing previous import 'shinydashboard::renderValueBox' by 'flexdashboard::renderValueBox' when loading 'protGear'
Warning: replacing previous import 'shinydashboard::valueBox' by 'flexdashboard::valueBox' when loading 'protGear'
Warning: replacing previous import 'shinydashboard::valueBoxOutput' by 'flexdashboard::valueBoxOutput' when loading 'protGear'
Warning in .f(.x[[i]], ...) :
KK2-17_first Not found in the sampleID files here
Warning in .f(.x[[i]], ...) :
KK2-18 Not found in the sampleID files here
Warning in .f(.x[[i]], ...) :
KK2-19 Not found in the sampleID files here
Warning in .f(.x[[i]], ...) :
KK2-20 Not found in the sampleID files here
Warning in .f(.x[[i]], ...) :
KK2-21 Not found in the sampleID files here
Warning in .f(.x[[i]], ...) :
KK2-17_first.csv Not found in the sampleID files
Warning in .f(.x[[i]], ...) :
KK2-18.csv Not found in the sampleID files
Warning in .f(.x[[i]], ...) :
KK2-19.csv Not found in the sampleID files
Warning in .f(.x[[i]], ...) :
KK2-20.csv Not found in the sampleID files
Warning in .f(.x[[i]], ...) :
KK2-21.csv Not found in the sampleID files
Adding missing grouping variables: `row`
Adding missing grouping variables: `row`
Adding missing grouping variables: `row`
Adding missing grouping variables: `row`
Adding missing grouping variables: `row`
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Problem with `mutate()` column `Array`.
i `Array = group_indices()`.
i `group_indices()` was deprecated in dplyr 1.0.0.
Please use `cur_group_id()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
i The warning occurred in group 1: slide = "KK2-17_first".
Warning in terms.formula(formula, data = data) :
'varlist' has changed (from nvar=26) to new 27 after EncodeVars() -- should no longer happen!
Warning in rlm.default(x, y, weights, method = method, wt.method = wt.method, :
'rlm' failed to converge in 20 steps
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 2 rows containing non-finite values (stat_cor).
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 2 rows containing non-finite values (stat_smooth).
Warning: Removed 2 rows containing missing values (geom_point).
Note: Using an external vector in selections is ambiguous.
i Use `all_of(control_antigens)` instead of `control_antigens` to silence this message.
i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This message is displayed once per session.
Quitting from lines 551-565 (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Graphics API version mismatch
--- failed re-building ‘vignette.Rmd’
SUMMARY: processing the following file failed:
‘vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
===============================
BiocCheckGitClone('protGear')
===============================
This is BiocCheckGitClone version 1.31.23. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
protGear.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
Summary:
ERROR count: 2
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2460/protGear_20220113190044/protGear.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘protGear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘protGear’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'limma', 'magrittr', 'ggplot2', 'tidyr', 'data.table', 'ggpubr',
'gtools', 'gridExtra', 'tibble', 'rlang', 'rmarkdown', 'knitr',
'vsn', 'genefilter', 'readr', 'Biobase', 'plyr', 'dplyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [16s/16s] WARNING
Found the following significant warnings:
Warning: replacing previous import ‘magrittr::set_names’ by ‘rlang::set_names’ when loading ‘protGear’
Warning: replacing previous import ‘gtools::chr’ by ‘rlang::chr’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘protGear’
Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘protGear’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘protGear’
Warning: replacing previous import ‘stats::lag’ by ‘dplyr::lag’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::renderValueBox’ by ‘flexdashboard::renderValueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBox’ by ‘flexdashboard::valueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBoxOutput’ by ‘flexdashboard::valueBoxOutput’ when loading ‘protGear’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2460/protGear_20220113190044/protGear.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 12.2Mb
sub-directories of 1Mb or more:
doc 4.2Mb
extdata 6.7Mb
shiny-examples 1.1Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘rlang’ ‘factoextra’
A package should be listed in only one of these fields.
* 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Biobase’ ‘gridExtra’ ‘knitr’ ‘vsn’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘dplyr:::select’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] 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’
remove_batch_effect: no visible binding for global variable ‘bts’
remove_batch_effect: no visible binding for global variable ‘site’
remove_batch_effect: no visible binding for global variable
‘exprs_antigen_vsn’
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 bts buffers
day_batches exprs_antigen_vsn 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 site slide stdev_all_anti temp v1 v2 val
value variable x xbar
* checking Rd files ... [0s/0s] NOTE
prepare_Rd: error_replicates.Rd:18-20: Dropping empty section \examples
prepare_Rd: launch_select.Rd:18-20: Dropping empty section \examples
prepare_Rd: remove_batch_effect.Rd:15-17: Dropping empty section \examples
prepare_Rd: rlm_normalise.Rd:18-20: Dropping empty section \examples
prepare_Rd: rlm_normalise_matrix.Rd:22-24: Dropping empty section \examples
* checking Rd metadata ... ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/23s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘scales’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 7 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2460/protGear_20220113190044/protGear.Rcheck/00check.log’
for details.
===============================
BiocCheck('protGear_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.23. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
Warning: replacing previous import ‘magrittr::set_names’ by ‘rlang::set_names’ when loading ‘protGear’
Warning: replacing previous import ‘gtools::chr’ by ‘rlang::chr’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘protGear’
Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘protGear’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘protGear’
Warning: replacing previous import ‘stats::lag’ by ‘dplyr::lag’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::renderValueBox’ by ‘flexdashboard::renderValueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBox’ by ‘flexdashboard::valueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBoxOutput’ by ‘flexdashboard::valueBoxOutput’ when loading ‘protGear’
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 119 object(s) are initialized.
Maybe they are part of a data set loaded with data(), or perhaps
part of an object referenced in with() or within().
function (object)
best_CV_estimation (x)
best_CV_estimation (prop)
best_CV_estimation (val)
best_CV_estimation (meanX1_X2)
best_CV_estimation (meanX2_X3)
best_CV_estimation (xbar)
best_CV_estimation (CVX)
best_CV_estimation (meanX)
best_CV_estimation (selected)
best_CV_estimation (CVX2_X3)
best_CV_estimation (CVX1_X3)
best_CV_estimation (CVX1_X2)
best_CV_estimation (best_CV)
best_CV_estimation (FMedianBG_correct)
bg_correct (sampleID)
bg_correct (Name)
bg_correct (antigen)
bg_correct (sample_array_ID)
bg_correct (Block)
bg_correct (Column)
bg_correct (Row)
bg_correct (FMedian)
bg_correct (FMedianBG_correct)
bg_correct (global_BGMedian)
bg_correct (minimum_BGMedian)
bg_correct (BGMedian)
buffer_spots (sampleID)
buffer_spots (antigen)
buffer_spots (FMedianBG_correct)
buffer_spots (Block)
buffer_spots (Column)
buffer_spots (Row)
cv_by_sample_estimation (variable)
cv_by_sample_estimation (value)
cv_by_sample_estimation (temp)
cv_estimation (FMedianBG_correct)
cv_estimation (sdX)
cv_estimation (meanX)
cv_estimation (sdX2_X3)
cv_estimation (meanX2_X3)
cv_estimation (sdX1_X3)
cv_estimation (meanX1_X3)
cv_estimation (sdX1_X2)
cv_estimation (meanX1_X2)
cv_estimation (CVX)
cv_estimation (CVX2_X3)
cv_estimation (CVX1_X3)
cv_estimation (CVX1_X2)
cv_estimation (antigen)
cv_estimation (sampleID)
cv_estimation (sample_array_ID)
extract_bg (v1)
extract_bg (v2)
extract_bg (index)
extract_bg (Name)
extract_bg (Block)
extract_bg (antigen)
matrix_normalise (day_batches)
matrix_normalise (machines)
matrix_normalise (variable)
matrix_normalise (value)
matrix_normalise (antigen)
matrix_normalise (sampleID2)
matrix_normalise (temp)
merge_sampleID (v1)
merge_sampleID (v2)
merge_sampleID (index)
merge_sampleID (Name)
plot_bg (.id)
plot_buffer (buffers)
plot_FB (.id)
plot_FB (log_fb)
plot_FB (log_bg)
plot_FB (antigen)
plot_FB (FBG_Median)
plot_FB (BG_Median)
plot_normalised (mean_all_anti)
plot_normalised (rank_mean_all_anti)
plot_normalised (stdev_all_anti)
plot_normalised_antigen (antigen)
plot_normalised_antigen (MFI)
plot_normalised_antigen (mean_mfi)
plot_normalised_antigen (rank_mean_all_anti)
plot_normalised_antigen (sd_mfi)
read_array_files (Block)
read_array_files (global_BGMedian)
read_array_files (minimum_BGMedian)
remove_batch_effect (bts)
remove_batch_effect (site)
remove_batch_effect (exprs_antigen_vsn)
rlm_normalise (Description)
rlm_normalise (Array)
rlm_normalise (Block)
rlm_normalise (antigen)
rlm_normalise (MFI_val)
rlm_normalise (antigen_name)
rlm_normalise (meanBest2_RLM)
rlm_normalise (sample_index)
rlm_normalise (slide)
rlm_normalise (sampleID2)
rlm_normalise_matrix (slide)
rlm_normalise_matrix (sample_index)
rlm_normalise_matrix (antigen)
rlm_normalise_matrix (MFI_val)
rlm_normalise_matrix (sample_array_ID)
rlm_normalise_matrix (Block)
tag_subtract (TAG)
tag_subtract (TAG_name)
tag_subtract (TAG_mfi)
visualize_slide (Block)
visualize_slide (X)
visualize_slide (Y)
visualize_slide (meanX)
visualize_slide (meanY)
visualize_slide_2d (Block)
visualize_slide_2d (X)
visualize_slide_2d (Y)
visualize_slide_2d (meanX)
visualize_slide_2d (meanY)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1 to 4.2.0.
* Checking package size...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 9.7444 MB
Size Requirement: 5.0000 MB
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, ChipOnChip, Metabolomics, Epigenetics,
Cheminformatics, Transcriptomics, Bayesian, Clustering,
Regression, ExonArray, GeneExpression, RNASeq, TwoChannel,
MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, CellBiology,
FunctionalGenomics, SystemsBiology, ImmunoOncology,
AlternativeSplicing, DifferentialExpression,
DifferentialSplicing, GeneSetEnrichment, MultipleComparison,
QualityControl, TimeCourse, DataImport
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of protGear...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
buffer_spot_functions.R (line 19, column 24)
cv_estimation_tag_functions.R (line 152, column 18)
normalisation_functions.R (line 256, column 25)
normalisation_functions.R (line 275, column 24)
normalisation_functions.R (line 280, column 24)
normalisation_functions.R (line 287, column 24)
normalisation_functions.R (line 306, column 13)
normalisation_functions.R (line 309, column 15)
normalisation_functions.R (line 365, column 10)
read_files_functions.R (line 113, column 34)
read_files_functions.R (line 114, column 50)
read_files_functions.R (line 132, column 20)
read_files_functions.R (line 150, column 25)
read_files_functions.R (line 173, column 24)
read_files_functions.R (line 389, column 24)
read_files_functions.R (line 407, column 26)
read_files_functions.R (line 419, column 33)
read_files_functions.R (line 432, column 26)
read_files_functions.R (line 445, column 26)
read_files_functions.R (line 462, column 26)
read_files_functions.R (line 476, column 26)
read_files_functions.R (line 503, column 35)
read_files_functions.R (line 529, column 33)
read_files_functions.R (line 590, column 34)
read_files_functions.R (line 590, column 83)
read_files_functions.R (line 606, column 20)
read_files_functions.R (line 624, column 25)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/cv_estimation_tag_functions.R (line 67, column 11)
print() in R/global_functions.R (line 165, column 3)
print() in R/normalisation_functions.R (line 152, column 5)
print() in R/read_files_functions.R (line 128, column 5)
print() in R/read_files_functions.R (line 602, column 5)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/cv_estimation_tag_functions.R (line 40, column 17)
R/cv_estimation_tag_functions.R (line 65, column 17)
R/global_functions.R (line 128, column 17)
R/read_files_functions.R (line 57, column 16)
R/read_files_functions.R (line 112, column 13)
R/read_files_functions.R (line 589, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 8 functions > 50 lines.
The longest 5 functions are:
rlm_normalise() (R/normalisation_functions.R, line 212): 197
lines
bg_correct() (R/read_files_functions.R, line 373): 162 lines
matrix_normalise() (R/normalisation_functions.R, line 36): 100
lines
cv_estimation() (R/cv_estimation_tag_functions.R, line 22): 84
lines
extract_bg() (R/read_files_functions.R, line 103): 76 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
launch_protGear_interactive.Rd, launch_select.Rd,
remove_batch_effect.Rd, rlm_normalise_matrix.Rd, rlm_normalise.Rd
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 408 lines (11%) are > 80 characters
long.
First 6 lines:
R/buffer_spot_functions.R:4 #' @param buffer_spot A character string co...
R/buffer_spot_functions.R:7 #' @description A function to extract the b...
R/buffer_spot_functions.R:13 #' bg_correct_df <- readr::read_csv(system...
R/buffer_spot_functions.R:47 #' @param buffer_names A character string ...
R/buffer_spot_functions.R:48 #' @param buffer_mfi A character string co...
R/buffer_spot_functions.R:50 #' @param slide_id A character string con...
* NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain
tabs.
First 4 lines:
R/read_files_functions.R:186 #' @param df A default dataset to use for...
R/read_files_functions.R:189 #' @param log_mfi a logical value indicat...
R/read_files_functions.R:272 #' @param log_mfi a logical value indicat...
R/read_files_functions.R:342 #' @param method a description of the bac...
* NOTE: Consider multiples of 4 spaces for line indents, 867
lines(23%) are not.
First 6 lines:
R/buffer_spot_functions.R:16 Data2_buffer <- Data1 %>%
R/buffer_spot_functions.R:22 antigen,
R/buffer_spot_functions.R:23 replicate,
R/buffer_spot_functions.R:24 FMedianBG_correct,
R/buffer_spot_functions.R:25 Block,
R/buffer_spot_functions.R:26 Column,
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 2
WARNING count: 0
NOTE count: 13
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.