nebbiolo2 Summary
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Package: TSAR |
Version: 0.99.10 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TSAR |
BuildTime: 1 minutes 30.77 seconds |
CheckCommand: BiocCheckGitClone('TSAR') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3113/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR.install-out.txt TSAR_0.99.10.tar.gz && BiocCheck('TSAR_0.99.10.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 21.33 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 3639.31 KiB |
BuildID:: TSAR_20230927193255 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: TSAR. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘TSAR/DESCRIPTION’ ... OK
* preparing ‘TSAR’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘TSAR_0.99.10.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('TSAR')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: TSAR
─ PackageVersion: 0.99.10
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSAR’ version ‘0.99.10’
* 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 ‘TSAR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... 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 ... [13s/13s] NOTE
TSA_Tms : <anonymous>: no visible binding for global variable ‘well_ID’
TSA_Tms : <anonymous>: no visible binding for global variable ‘Tm’
TSA_Tms : <anonymous>: no visible global function definition for ‘sd’
TSA_Tms: no visible binding for global variable ‘well_ID’
TSA_Tms: no visible binding for global variable ‘Tm’
TSA_Tms: no visible binding for global variable ‘condition_ID’
TSA_Tms: no visible binding for global variable ‘Protein’
TSA_Tms: no visible binding for global variable ‘Ligand’
TSA_average: no visible binding for global variable ‘Temperature’
TSA_average: no visible binding for global variable ‘Fluorescence’
TSA_average: no visible global function definition for ‘sd’
TSA_average: no visible binding for global variable ‘Normalized’
TSA_average: no visible global function definition for ‘predict’
TSA_boxplot: no visible binding for global variable ‘condition_ID’
TSA_boxplot: no visible binding for global variable ‘Tm’
TSA_boxplot: no visible binding for global variable ‘Ligand’
TSA_boxplot: no visible binding for global variable ‘well_ID’
TSA_boxplot: no visible binding for global variable ‘Protein’
TSA_compare_plot: no visible binding for global variable ‘Temperature’
TSA_compare_plot: no visible binding for global variable ‘avg_smooth’
TSA_compare_plot: no visible binding for global variable
‘sd_min_smooth’
TSA_compare_plot: no visible binding for global variable
‘sd_max_smooth’
TSA_compare_plot: no visible global function definition for
‘colorRampPalette’
TSA_wells_plot: no visible binding for global variable ‘Temperature’
TSA_wells_plot: no visible binding for global variable ‘Fluorescence’
TSA_wells_plot: no visible binding for global variable ‘Normalized’
TSA_wells_plot: no visible binding for global variable ‘well_ID’
TSA_wells_plot: no visible binding for global variable ‘sd_min_smooth’
TSA_wells_plot: no visible binding for global variable ‘sd_max_smooth’
TSA_wells_plot: no visible binding for global variable ‘avg_smooth’
TSA_wells_plot: no visible binding for global variable ‘sd_min’
TSA_wells_plot: no visible binding for global variable ‘sd_max’
TSA_wells_plot: no visible binding for global variable ‘average’
build_curves: no visible binding for global variable ‘condition_ID’
build_table: no visible global function definition for ‘head’
build_well: no visible global function definition for ‘head’
dummy_plot: no visible binding for global variable ‘x’
dummy_plot: no visible binding for global variable ‘y’
gam_analysis: no visible global function definition for ‘all_of’
join_well_info: no visible binding for global variable ‘Col’
join_well_info: no visible binding for global variable ‘pos’
join_well_info: no visible binding for global variable ‘Well’
join_well_info: no visible binding for global variable ‘Protein’
join_well_info: no visible binding for global variable ‘Ligand’
join_well_info: no visible global function definition for ‘na.omit’
merge_norm : <anonymous>: no visible global function definition for
‘read.csv’
merge_norm : <anonymous>: no visible binding for global variable
‘Well.Position’
merge_norm : <anonymous>: no visible binding for global variable
‘Protein’
merge_norm : <anonymous>: no visible binding for global variable
‘Ligand’
merge_norm: no visible binding for global variable ‘tm’
merge_norm: no visible binding for global variable ‘Well.Position’
merge_update: no visible global function definition for ‘na.omit’
model_boltzmann: no visible binding for global variable ‘Temperature’
normalize: no visible global function definition for ‘all_of’
preview_condition: no visible global function definition for ‘head’
preview_model: no visible binding for global variable ‘Well.Position’
read_analysis: no visible global function definition for ‘read.delim’
read_analysis: no visible global function definition for ‘read.csv’
read_raw_data: no visible global function definition for ‘read.delim’
read_raw_data: no visible global function definition for ‘read.csv’
remove_raw: no visible binding for global variable ‘Well.Position’
remove_raw: no visible binding for global variable ‘Well’
remove_selected_graph: no visible binding for global variable
‘condition_ID’
remove_selected_graph: no visible binding for global variable ‘well_ID’
screen: no visible binding for global variable ‘Well.Position’
screen: no visible binding for global variable ‘Well’
screen: no visible binding for global variable ‘Temperature’
screen: no visible binding for global variable ‘Fluorescence’
view_deriv: no visible binding for global variable ‘Temperature’
view_deriv: no visible binding for global variable ‘norm_deriv’
view_deriv: no visible binding for global variable ‘well_ID’
view_deriv: no visible binding for global variable ‘Tm’
view_model: no visible binding for global variable ‘Temperature’
view_model: no visible binding for global variable ‘Normalized’
view_model: no visible binding for global variable ‘fitted’
view_model: no visible global function definition for ‘na.omit’
view_model: no visible binding for global variable ‘norm_deriv’
view_model: no visible binding for global variable ‘Well.Position’
Undefined global functions or variables:
Col Fluorescence Ligand Normalized Protein Temperature Tm Well
Well.Position all_of average avg_smooth colorRampPalette condition_ID
fitted head na.omit norm_deriv pos predict read.csv read.delim sd
sd_max sd_max_smooth sd_min sd_min_smooth tm well_ID x y
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "fitted", "na.omit", "predict", "sd")
importFrom("utils", "head", "read.csv", "read.delim")
to your NAMESPACE file.
Found the following assignments to the global environment:
File ‘TSAR/R/observers_analyze.R’:
assign(input$name, output_data(), envir = .GlobalEnv)
File ‘TSAR/R/observers_graph.R’:
assign("tsar_data", graph_tsar_data(), envir = .GlobalEnv)
File ‘TSAR/R/observers_weed.R’:
assign("new_raw_data", dataset(), envir = .GlobalEnv)
* checking Rd files ... [0s/0s] OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/57s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TSA_wells_plot 11.880 0.159 12.041
gam_analysis 9.755 0.196 9.951
view_deriv 5.167 0.225 5.367
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/11s]
[12s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* 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 ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR.Rcheck/00check.log’
for details.
===============================
BiocCheck('TSAR_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: TSAR
─ PackageVersion: 0.99.10
─ sourceDir: /tmp/RtmpIqvyqn/file2f4f68671bca02/TSAR
─ installDir: /tmp/RtmpIqvyqn/file2f4f68785b0fb9
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* 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...
* 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 recommeded fields in DESCRIPTION...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of TSAR...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 13 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 178 lines
(2%) are not.
See https://contributions.bioconductor.org/r-code.html
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 7 NOTES
See the TSAR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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lconway Summary
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Package: TSAR |
Version: 0.99.10 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TSAR |
BuildTime: 1 minutes 40.97 seconds |
CheckCommand: BiocCheckGitClone('TSAR') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3113/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR.install-out.txt TSAR_0.99.10.tar.gz && BiocCheck('TSAR_0.99.10.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 36.10 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh TSAR_0.99.10.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 14.76 seconds |
PackageFileSize: 3671.57 KiB |
BuildID:: TSAR_20230927193255 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: TSAR. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘TSAR/DESCRIPTION’ ... OK
* preparing ‘TSAR’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘TSAR_0.99.10.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('TSAR')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: TSAR
─ PackageVersion: 0.99.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSAR’ version ‘0.99.10’
* 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 ‘TSAR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... 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 ... [14s/14s] NOTE
TSA_Tms : <anonymous>: no visible binding for global variable ‘well_ID’
TSA_Tms : <anonymous>: no visible binding for global variable ‘Tm’
TSA_Tms : <anonymous>: no visible global function definition for ‘sd’
TSA_Tms: no visible binding for global variable ‘well_ID’
TSA_Tms: no visible binding for global variable ‘Tm’
TSA_Tms: no visible binding for global variable ‘condition_ID’
TSA_Tms: no visible binding for global variable ‘Protein’
TSA_Tms: no visible binding for global variable ‘Ligand’
TSA_average: no visible binding for global variable ‘Temperature’
TSA_average: no visible binding for global variable ‘Fluorescence’
TSA_average: no visible global function definition for ‘sd’
TSA_average: no visible binding for global variable ‘Normalized’
TSA_average: no visible global function definition for ‘predict’
TSA_boxplot: no visible binding for global variable ‘condition_ID’
TSA_boxplot: no visible binding for global variable ‘Tm’
TSA_boxplot: no visible binding for global variable ‘Ligand’
TSA_boxplot: no visible binding for global variable ‘well_ID’
TSA_boxplot: no visible binding for global variable ‘Protein’
TSA_compare_plot: no visible binding for global variable ‘Temperature’
TSA_compare_plot: no visible binding for global variable ‘avg_smooth’
TSA_compare_plot: no visible binding for global variable
‘sd_min_smooth’
TSA_compare_plot: no visible binding for global variable
‘sd_max_smooth’
TSA_compare_plot: no visible global function definition for
‘colorRampPalette’
TSA_wells_plot: no visible binding for global variable ‘Temperature’
TSA_wells_plot: no visible binding for global variable ‘Fluorescence’
TSA_wells_plot: no visible binding for global variable ‘Normalized’
TSA_wells_plot: no visible binding for global variable ‘well_ID’
TSA_wells_plot: no visible binding for global variable ‘sd_min_smooth’
TSA_wells_plot: no visible binding for global variable ‘sd_max_smooth’
TSA_wells_plot: no visible binding for global variable ‘avg_smooth’
TSA_wells_plot: no visible binding for global variable ‘sd_min’
TSA_wells_plot: no visible binding for global variable ‘sd_max’
TSA_wells_plot: no visible binding for global variable ‘average’
build_curves: no visible binding for global variable ‘condition_ID’
build_table: no visible global function definition for ‘head’
build_well: no visible global function definition for ‘head’
dummy_plot: no visible binding for global variable ‘x’
dummy_plot: no visible binding for global variable ‘y’
gam_analysis: no visible global function definition for ‘all_of’
join_well_info: no visible binding for global variable ‘Col’
join_well_info: no visible binding for global variable ‘pos’
join_well_info: no visible binding for global variable ‘Well’
join_well_info: no visible binding for global variable ‘Protein’
join_well_info: no visible binding for global variable ‘Ligand’
join_well_info: no visible global function definition for ‘na.omit’
merge_norm : <anonymous>: no visible global function definition for
‘read.csv’
merge_norm : <anonymous>: no visible binding for global variable
‘Well.Position’
merge_norm : <anonymous>: no visible binding for global variable
‘Protein’
merge_norm : <anonymous>: no visible binding for global variable
‘Ligand’
merge_norm: no visible binding for global variable ‘tm’
merge_norm: no visible binding for global variable ‘Well.Position’
merge_update: no visible global function definition for ‘na.omit’
model_boltzmann: no visible binding for global variable ‘Temperature’
normalize: no visible global function definition for ‘all_of’
preview_condition: no visible global function definition for ‘head’
preview_model: no visible binding for global variable ‘Well.Position’
read_analysis: no visible global function definition for ‘read.delim’
read_analysis: no visible global function definition for ‘read.csv’
read_raw_data: no visible global function definition for ‘read.delim’
read_raw_data: no visible global function definition for ‘read.csv’
remove_raw: no visible binding for global variable ‘Well.Position’
remove_raw: no visible binding for global variable ‘Well’
remove_selected_graph: no visible binding for global variable
‘condition_ID’
remove_selected_graph: no visible binding for global variable ‘well_ID’
screen: no visible binding for global variable ‘Well.Position’
screen: no visible binding for global variable ‘Well’
screen: no visible binding for global variable ‘Temperature’
screen: no visible binding for global variable ‘Fluorescence’
view_deriv: no visible binding for global variable ‘Temperature’
view_deriv: no visible binding for global variable ‘norm_deriv’
view_deriv: no visible binding for global variable ‘well_ID’
view_deriv: no visible binding for global variable ‘Tm’
view_model: no visible binding for global variable ‘Temperature’
view_model: no visible binding for global variable ‘Normalized’
view_model: no visible binding for global variable ‘fitted’
view_model: no visible global function definition for ‘na.omit’
view_model: no visible binding for global variable ‘norm_deriv’
view_model: no visible binding for global variable ‘Well.Position’
Undefined global functions or variables:
Col Fluorescence Ligand Normalized Protein Temperature Tm Well
Well.Position all_of average avg_smooth colorRampPalette condition_ID
fitted head na.omit norm_deriv pos predict read.csv read.delim sd
sd_max sd_max_smooth sd_min sd_min_smooth tm well_ID x y
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "fitted", "na.omit", "predict", "sd")
importFrom("utils", "head", "read.csv", "read.delim")
to your NAMESPACE file.
Found the following assignments to the global environment:
File ‘TSAR/R/observers_analyze.R’:
assign(input$name, output_data(), envir = .GlobalEnv)
File ‘TSAR/R/observers_graph.R’:
assign("tsar_data", graph_tsar_data(), envir = .GlobalEnv)
File ‘TSAR/R/observers_weed.R’:
assign("new_raw_data", dataset(), envir = .GlobalEnv)
* checking Rd files ... [1s/1s] OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [55s/56s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TSA_wells_plot 11.052 0.100 11.209
gam_analysis 8.278 0.724 9.097
view_deriv 4.876 0.458 5.450
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/13s]
[13s/13s] OK
* checking for unstated dependencies in vignettes ... OK
* 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 ... [7s/8s] OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR.Rcheck/00check.log’
for details.
===============================
BiocCheck('TSAR_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: TSAR
─ PackageVersion: 0.99.10
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpMThK3x/file73f97a416afa/TSAR
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpMThK3x/file73f96e32464
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3113/03f64e9734fcd772a1df6d36859d355b5d55ae72/TSAR.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* 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...
* 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 recommeded fields in DESCRIPTION...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of TSAR...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 13 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 178 lines
(2%) are not.
See https://contributions.bioconductor.org/r-code.html
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 7 NOTES
See the TSAR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir TSAR_0.99.10.tar.gz'
>>>>>>>
* installing *source* package ‘TSAR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (TSAR)