Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘LipidSigR/DESCRIPTION’ ... OK
* preparing ‘LipidSigR’:
* 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 ‘LipidSigR_0.99.7.tar.gz’

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 BiocCheckGitClone('LipidSigR')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.7
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2631/ae71406051d208cb520b5367b90f6184b51d616e/LipidSigR
─ 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/2631/ae71406051d208cb520b5367b90f6184b51d616e/LipidSigR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LipidSigR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LipidSigR’ version ‘0.99.7’
* 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 ‘LipidSigR’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [32s/35s] OK
* checking Rd files ... [1s/2s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [84s/87s] ERROR
Running examples in ‘LipidSigR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SHAP
> ### Title: SHAP
> ### Aliases: SHAP
> 
> ### ** Examples
> 
> library(SHAPforxgboost)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> data("ML_exp_data")
> data("ML_lipid_char_table")
> data("ML_condition_table")
> condition_table <- ML_condition_table[85:144, ]
> exp_data <- ML_exp_data[1:40, ] %>%
+   select(feature, condition_table$sample_name)
> lipid_char_table <- ML_lipid_char_table[1:40, ]
> char_var <- colnames(lipid_char_table)[-1]
> ML_data <- ML_data_process(exp_data, group_info = condition_table,
+                            lipid_char_table, char_var[1],
+                            exclude_var_missing=TRUE, missing_pct_limit=50,
+                            replace_zero=TRUE, zero2what='min', xmin=0.5,
+                            replace_NA=TRUE, NA2what='min', ymin=0.5,
+                            pct_transform=TRUE, data_transform=TRUE,
+                            trans_type='log', centering=FALSE, scaling=FALSE)
> ML_output <- ML_final(ML_data[[2]], ranking_method='Random_forest',
+                       ML_method='Random_forest', split_prop=0.3, nfold=3)
[1] "CV fold 1 done"
[1] "CV fold 2 done"
[1] "CV fold 3 done"
> SHAP(ML_data[[2]], best_model=ML_output[[8]],
+      best_model_feature=ML_output[[9]],
+      ML_method='Random_forest', feature_n=10, nsim=5, plotly=TRUE)
Error in loadNamespace(x) : there is no package called ‘fastshap’
Calls: SHAP ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [212s/168s]
 [212s/168s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  Iteration 350: error is 0.542852 (50 iterations in 0.00 seconds)
  Iteration 400: error is 0.285678 (50 iterations in 0.00 seconds)
  Iteration 450: error is 0.228041 (50 iterations in 0.00 seconds)
  Iteration 500: error is 0.224977 (50 iterations in 0.00 seconds)
  Fitting performed in 0.01 seconds.
  [ FAIL 1 | WARN 90 | SKIP 0 | PASS 116 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_ML.R:91'): Feature importance function computed successfullly. ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'fastshap'
  Backtrace:
      ▆
   1. ├─LipidSigR::SHAP(...) at test_ML.R:91:2
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 90 | SKIP 0 | PASS 116 ]
  Error: Test failures
  Execution halted
* 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 ... [16s/18s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode character ∂ (U+2202)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE

Status: 3 ERRORs, 1 WARNING
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2631/ae71406051d208cb520b5367b90f6184b51d616e/LipidSigR.Rcheck/00check.log’
for details.





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 BiocCheck('LipidSigR_0.99.7.tar.gz')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.7
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp4KBC7l/file994d284af42f/LipidSigR
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp4KBC7l/file994d7e7954a2
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2631/ae71406051d208cb520b5367b90f6184b51d616e/LipidSigR.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...
    * NOTE: Update R version dependency from 4.0.0 to 4.3.0.
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking 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 LipidSigR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 89 functions greater than 50 lines.
* Checking man page documentation...
* 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; 50 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 5791 lines
      (35%) 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 | 4 NOTES

See the LipidSigR.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 LipidSigR_0.99.7.tar.gz'
>>>>>>> 

* installing *source* package ‘LipidSigR’ ...
** 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 (LipidSigR)