merida1 Summary
[top]
Package: protGear |
Version: 0.99.543 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data protGear |
BuildTime: 2 minutes 8.19 seconds |
CheckCommand: BiocCheckGitClone('protGear') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch protGear_0.99.543.tar.gz && BiocCheck('protGear_0.99.543.tar.gz', `new-package`=TRUE) |
CheckTime: 6 minutes 34.33 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh protGear_0.99.543.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 45.70 seconds |
PackageFileSize: 4775.89 KiB |
BuildID:: protGear_20220214111613 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: protGear. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 1. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘protGear/DESCRIPTION’ ... OK
* preparing ‘protGear’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘protGear_0.99.543.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('protGear')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
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
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2460/68f55e7a4a273c5be024aeba93cdbd4a9062dcdc/protGear.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ‘0.99.543’
* 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', 'Kendall', '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 ... [49s/52s] OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 4.2Mb
extdata 1.2Mb
* 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’ ‘magrittr’ ‘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 ... [48s/49s] 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 global function definition for ‘:=’
read_array_files: no visible binding for global variable
‘global_BGMedian’
read_array_files: no visible global function definition for
‘parse_expr’
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 global function definition for ‘UQ’
tag_subtract: no visible global function definition for ‘:=’
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 UQ 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 parse_expr 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 ... [1s/1s] 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 ... [43s/43s] 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: 7 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2460/68f55e7a4a273c5be024aeba93cdbd4a9062dcdc/protGear.Rcheck/00check.log’
for details.
===============================
BiocCheck('protGear_0.99.543.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2460/68f55e7a4a273c5be024aeba93cdbd4a9062dcdc/protGear_0.99.543.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpUBSVeu/file1663c220a489/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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...
* 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...
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
* 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 153, 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 390, column 24)
read_files_functions.R (line 408, column 26)
read_files_functions.R (line 420, column 33)
read_files_functions.R (line 433, column 26)
read_files_functions.R (line 446, column 26)
read_files_functions.R (line 463, column 26)
read_files_functions.R (line 477, column 26)
read_files_functions.R (line 504, column 35)
read_files_functions.R (line 530, column 33)
read_files_functions.R (line 591, column 34)
read_files_functions.R (line 591, column 83)
read_files_functions.R (line 607, column 20)
read_files_functions.R (line 625, column 25)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/cv_estimation_tag_functions.R (line 68, 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 603, column 5)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/cv_estimation_tag_functions.R (line 41, column 17)
R/cv_estimation_tag_functions.R (line 66, 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 590, 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 374): 162 lines
matrix_normalise() (R/normalisation_functions.R, line 36): 100
lines
cv_estimation() (R/cv_estimation_tag_functions.R, line 23): 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; 411 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, 862
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 12
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
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir protGear_0.99.543.tar.gz'
>>>>>>>
* 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)
nebbiolo1 Summary
[top]
Package: protGear |
Version: 0.99.543 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data protGear |
BuildTime: 0 minutes 41.19 seconds |
CheckCommand: BiocCheckGitClone('protGear') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings protGear_0.99.543.tar.gz && BiocCheck('protGear_0.99.543.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 18.03 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 4795.74 KiB |
BuildID:: protGear_20220214111613 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: protGear. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 1. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘protGear/DESCRIPTION’ ... OK
* preparing ‘protGear’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘protGear_0.99.543.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('protGear')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
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
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2460/68f55e7a4a273c5be024aeba93cdbd4a9062dcdc/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 ‘0.99.543’
* 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', 'Kendall', '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] OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 3.7Mb
* 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’ ‘magrittr’ ‘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 global function definition for ‘:=’
read_array_files: no visible binding for global variable
‘global_BGMedian’
read_array_files: no visible global function definition for
‘parse_expr’
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 global function definition for ‘UQ’
tag_subtract: no visible global function definition for ‘:=’
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 UQ 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 parse_expr 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 ... [20s/20s] 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: 7 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2460/68f55e7a4a273c5be024aeba93cdbd4a9062dcdc/protGear.Rcheck/00check.log’
for details.
===============================
BiocCheck('protGear_0.99.543.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2460/68f55e7a4a273c5be024aeba93cdbd4a9062dcdc/protGear_0.99.543.tar.gz" "/tmp/Rtmp07dujA/file999ab3fbc6692/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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...
* 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...
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
* 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 153, 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 390, column 24)
read_files_functions.R (line 408, column 26)
read_files_functions.R (line 420, column 33)
read_files_functions.R (line 433, column 26)
read_files_functions.R (line 446, column 26)
read_files_functions.R (line 463, column 26)
read_files_functions.R (line 477, column 26)
read_files_functions.R (line 504, column 35)
read_files_functions.R (line 530, column 33)
read_files_functions.R (line 591, column 34)
read_files_functions.R (line 591, column 83)
read_files_functions.R (line 607, column 20)
read_files_functions.R (line 625, column 25)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/cv_estimation_tag_functions.R (line 68, 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 603, column 5)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/cv_estimation_tag_functions.R (line 41, column 17)
R/cv_estimation_tag_functions.R (line 66, 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 590, 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 374): 162 lines
matrix_normalise() (R/normalisation_functions.R, line 36): 100
lines
cv_estimation() (R/cv_estimation_tag_functions.R, line 23): 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; 411 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, 862
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 12
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
nebbiolo1 BUILD BIN output
[top]