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_0.99.4.tar.gz’

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 BiocCheckGitClone('LipidSigR')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2631/fb92beef550964bc884379902f1a0df62fdea91e/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/fb92beef550964bc884379902f1a0df62fdea91e/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 ‘0.99.4’
* 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘igraph’ ‘tidygraph’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [33s/36s] NOTE
DE_char_2: no visible global function definition for
  ‘stat_compare_means’
DE_species_2: no visible binding for global variable ‘A’
DE_species_2: no visible binding for global variable
  ‘sig_log2fc.pvalue_colors’
DE_sub_char_plot_2: no visible global function definition for
  ‘stat_compare_means’
PLSDA: no visible binding for global variable ‘x0’
PLSDA: no visible binding for global variable ‘y0’
PLSDA: no visible binding for global variable ‘r’
PLSDA: no visible binding for global variable ‘x’
PLSDA: no visible binding for global variable ‘y’
PR_plot_all: no visible binding for global variable ‘feature_num_label’
ROC_plot_all: no visible binding for global variable
  ‘feature_num_label’
SHAP_dependence_plot: no visible binding for global variable ‘a’
SHAP_dependence_plot: no visible binding for global variable ‘b’
cor_network: no visible binding for global variable ‘name’
cor_network: no visible binding for global variable ‘Feature
  importance’
evalution_plot: no visible binding for global variable ‘sd_value’
evalution_plot: no visible binding for global variable ‘lower’
evalution_plot: no visible binding for global variable ‘upper’
evalution_plot: no visible binding for global variable ‘highest’
exp_profiling: no visible binding for global variable ‘expr.count’
exp_profiling: no visible binding for global variable ‘lipid_amount’
Undefined global functions or variables:
  A Feature importance a b expr.count feature_num_label highest
  lipid_amount lower name r sd_value sig_log2fc.pvalue_colors
  stat_compare_means upper x x0 y y0
* 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 ... WARNING
Data codoc mismatches from documentation object 'corr_exp_data':
Variables in data frame 'corr_exp_data'
  Code: feature sample1 sample10 sample100 sample101 sample102
        sample103 sample104 sample105 sample106 sample107 sample108
        sample109 sample11 sample110 sample111 sample112 sample113
        sample114 sample115 sample116 sample117 sample118 sample119
        sample12 sample120 sample121 sample122 sample123 sample124
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        sample14 sample15 sample16 sample17 sample18 sample19 sample2
        sample20 sample21 sample22 sample23 sample24 sample25 sample26
        sample27 sample28 sample29 sample3 sample30 sample31 sample32
        sample33 sample34 sample35 sample36 sample37 sample38 sample39
        sample4 sample40 sample41 sample42 sample43 sample44 sample45
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        sample59 sample6 sample60 sample61 sample62 sample63 sample64
        sample65 sample66 sample67 sample68 sample69 sample7 sample70
        sample71 sample72 sample73 sample74 sample75 sample76 sample77
        sample78 sample79 sample8 sample80 sample81 sample82 sample83
        sample84 sample85 sample86 sample87 sample88 sample89 sample9
        sample90 sample91 sample92 sample93 sample94 sample95 sample96
        sample97 sample98 sample99
  Docs: feature sample1-129

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'cor_network'
  ‘plotly’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [45s/50s] ERROR
Running examples in ‘LipidSigR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ML_final
> ### Title: ML_final
> ### Aliases: ML_final
> 
> ### ** Examples
> 
> data("ML_exp_data")
> data("ML_lipid_char_table")
> data("ML_condition_table")
> lipid_char_table <- ML_lipid_char_table[1:40, ]
> condition_table <- ML_condition_table[85:144, ]
> exp_data <- ML_exp_data[1:40, ] %>%
+    select(feature, condition_table$sample_name)
Error in ML_exp_data[1:40, ] %>% select(feature, condition_table$sample_name) : 
  could not find function "%>%"
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [210s/164s]
 [210s/165s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  Iteration 150: error is 58.014102 (50 iterations in 0.00 seconds)
  Iteration 200: error is 50.572464 (50 iterations in 0.00 seconds)
  Iteration 250: error is 56.505902 (50 iterations in 0.00 seconds)
  Iteration 300: error is 0.953699 (50 iterations in 0.00 seconds)
  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:89'): Feature importance function computed successfullly. ──
  <packageNotFoundError/error/condition>
  Error in `library(SHAPforxgboost)`: there is no package called 'SHAPforxgboost'
  Backtrace:
      ▆
   1. └─base::library(SHAPforxgboost) at test_ML.R:89:2
  
  [ 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 ... [18s/21s] 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, 4 WARNINGs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2631/fb92beef550964bc884379902f1a0df62fdea91e/LipidSigR.Rcheck/00check.log’
for details.





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 BiocCheck('LipidSigR_0.99.4.tar.gz')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpwJApBA/fileae9f2138fc65/LipidSigR
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpwJApBA/fileae9fa13734
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2631/fb92beef550964bc884379902f1a0df62fdea91e/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; 48 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 5789 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_0.99.4.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)