Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘IntOMICS/DESCRIPTION’ ... OK
* preparing ‘IntOMICS’:
* 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 ‘IntOMICS_0.99.10.tar.gz’

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 BiocCheckGitClone('IntOMICS')

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─ BiocCheckVersion: 1.35.4
─ BiocVersion: 3.17
─ Package: IntOMICS
─ PackageVersion: 0.99.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2744/ad169637739545672b860467552d56625b0bd433/IntOMICS
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...

─ 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/2744/ad169637739545672b860467552d56625b0bd433/IntOMICS.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntOMICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IntOMICS’ 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 ‘IntOMICS’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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/32s] NOTE
dens_edge_weights: no visible binding for global variable ‘edge_weight’
dens_edge_weights: no visible binding for global variable ‘scaled’
ggraph_weighted_net: no visible binding for global variable
  ‘weighted_net_res’
ggraph_weighted_net: no visible binding for global variable
  ‘node2.degree’
ggraph_weighted_net: no visible binding for global variable ‘weight’
ggraph_weighted_net: no visible binding for global variable ‘color’
ggraph_weighted_net: no visible binding for global variable ‘label’
legend_custom_ggplot: no visible binding for global variable ‘x_min’
legend_custom_ggplot: no visible binding for global variable ‘x_max’
legend_custom_ggplot: no visible binding for global variable ‘y_min’
legend_custom_ggplot: no visible binding for global variable ‘y_max’
legend_custom_ggplot: no visible binding for global variable ‘x_lab’
legend_custom_ggplot: no visible binding for global variable ‘val’
Undefined global functions or variables:
  color edge_weight label node2.degree scaled val weight
  weighted_net_res x_lab x_max x_min y_max y_min
* 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 ... [13s/13s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] ERROR
Running examples in ‘IntOMICS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: b_prior_mat
> ### Title: biological prior matrix
> ### Aliases: b_prior_mat
> ### Keywords: internal
> 
> ### ** Examples
> 
> data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics", "gene_annot"),
+ package="IntOMICS")
> omics <- omics_to_list(omics = omics, gene_annot = gene_annot, 
+                        layers_def = layers_def)
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

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

    anyMissing, rowMedians

> B <- b_prior_mat(omics = omics, PK = PK, layers_def = layers_def, 
+      annot = annot, lm_METH = TRUE, r_squared_thres = 0.3,
+      p_val_thres = 0.05, TFtargs = TFtarg_mat, TFBS_belief = 0.75, 
+      nonGE_belief = 0.5,  woPKGE_belief = 0.5)
Error in if (any(regexpr("EID:", colnames(omics[[layers_def$omics[1]]])) <  : 
  missing value where TRUE/FALSE needed
Calls: b_prior_mat
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [14s/14s]
 [14s/14s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_missing_PK.R:4'): Output from omics_module ─────────────────────
  Error in `omics_module(omics = omics, layers_def = layers_def, TFtargs = TFtarg_mat, 
      annot = annot, gene_annot = gene_annot)`: Number of modalities differs in "omics" and "layers_def".
  Backtrace:
      ▆
   1. ├─testthat::expect_message(...) at test_missing_PK.R:4:2
   2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─IntOMICS::omics_module(...)
  ── Error ('test_omics_module.R:4'): output from omics_module is OK ─────────────
  Error in `omics_module(omics = omics, PK = PK, layers_def = layers_def, 
      TFtargs = TFtarg_mat, annot = annot, gene_annot = gene_annot)`: Number of modalities differs in "omics" and "layers_def".
  Backtrace:
      ▆
   1. └─IntOMICS::omics_module(...) at test_omics_module.R:4:2
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 11 ]
  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 ... [5s/5s] OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2744/ad169637739545672b860467552d56625b0bd433/IntOMICS.Rcheck/00check.log’
for details.





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 BiocCheck('IntOMICS_0.99.10.tar.gz')

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─ BiocCheckVersion: 1.35.4
─ BiocVersion: 3.17
─ Package: IntOMICS
─ PackageVersion: 0.99.10
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpTFgkzW/file78f26f993423/IntOMICS
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpTFgkzW/file78f218f9f0fe
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2744/ad169637739545672b860467552d56625b0bd433/IntOMICS.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 4.2.0 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* 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 IntOMICS...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in man/dens_edge_weights.Rd
    Found @ in man/ggraph_weighted_net.Rd
    Found @ in man/legend_custom_ggplot.Rd
    Found @ in man/weighted_net.Rd
    Found @ in vignettes/IntOMICS_vignette.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 132 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; 97 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 815 lines
      (11%) 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...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      Bioc-Devel mailing list (requires admin credentials). Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/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 | 9 NOTES

See the IntOMICS.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 IntOMICS_0.99.10.tar.gz'
>>>>>>> 

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