Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* 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_0.99.11.tar.gz’

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 BiocCheckGitClone('TSAR')

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─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: TSAR
─ PackageVersion: 0.99.11
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3113/561a75db58e890c4f5606ab1b9998f8050cc87d7/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')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3113/561a75db58e890c4f5606ab1b9998f8050cc87d7/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 ‘0.99.11’
* 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/3s] OK
* checking whether the package can be unloaded cleanly ... [2s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/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/15s] 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 : process_well: no visible binding for global variable
  ‘Well.Position’
gam_analysis : process_well: 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 : normalize_by_well: no visible binding for global variable
  ‘Well.Position’
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 ... [52s/54s] OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
TSA_wells_plot 10.288  0.119  10.545
gam_analysis    7.885  0.795   9.093
view_deriv      4.725  0.421   5.229
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/11s]
 [11s/11s] 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/3113/561a75db58e890c4f5606ab1b9998f8050cc87d7/TSAR.Rcheck/00check.log’
for details.






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 BiocCheck('TSAR_0.99.11.tar.gz')

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─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: TSAR
─ PackageVersion: 0.99.11
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpwWZGxs/file71f18f2391e/TSAR
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpwWZGxs/file71f7f5498d5
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3113/561a75db58e890c4f5606ab1b9998f8050cc87d7/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 14 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.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir TSAR_0.99.11.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)