Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘CBNplot/DESCRIPTION’ ... OK
* preparing ‘CBNplot’:
* 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 ‘CBNplot_0.99.1.tar.gz’

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 BiocCheckGitClone('CBNplot')

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This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2477/CBNplot_20220301151746/CBNplot.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CBNplot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CBNplot’ version ‘0.99.1’
* 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 ‘CBNplot’ can be installed ... [26s/26s] 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [29s/29s] NOTE
bngeneplot: warning in coord_flip(y = c(min(strengthTop$strength,
  strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
  'ylim'
bngeneplotCustom: warning in coord_flip(y = c(min(strengthTop$strength,
  strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
  'ylim'
bnpathplot: warning in coord_flip(y = c(min(strengthTop$strength,
  strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
  'ylim'
bnpathplotCustom: warning in coord_flip(y = c(min(strengthTop$strength,
  strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
  'ylim'
bngeneplot: no visible binding for global variable ‘cell_line’
bngeneplot: no visible binding for global variable ‘dependency’
bngeneplot: no visible binding for global variable ‘..count..’
bngeneplot: no visible binding for global variable ‘SYMBOL’
bngeneplot: no visible binding for global variable ‘Pathway’
bngeneplot: no visible binding for global variable ‘direction’
bngeneplot: no visible binding for global variable ‘label’
bngeneplot: no visible binding for global variable ‘value’
bngeneplot: no visible binding for global variable ‘name’
bngeneplot: no visible global function definition for ‘strength.viewer’
bngeneplot: no visible binding for global variable ‘gene_name’
bngeneplot : <anonymous>: no visible binding for global variable
  ‘gene_name’
bngeneplot: no visible binding for global variable ‘depmap_id’
bngeneplot: no visible binding for global variable ‘lineage’
bngeneplotCustom: no visible binding for global variable ‘cell_line’
bngeneplotCustom: no visible binding for global variable ‘direction’
bngeneplotCustom: no visible binding for global variable ‘label’
bngeneplotCustom: no visible binding for global variable ‘value’
bngeneplotCustom: no visible binding for global variable ‘name’
bngeneplotCustom: no visible binding for global variable ‘gene_name’
bngeneplotCustom : <anonymous>: no visible binding for global variable
  ‘gene_name’
bngeneplotCustom : <anonymous>: no visible binding for global variable
  ‘cls’
bnpathplot: no visible binding for global variable ‘cell_line’
bnpathplot: no visible binding for global variable ‘dependency’
bnpathplot: no visible binding for global variable ‘..count..’
bnpathplot: no visible binding for global variable ‘qvalue’
bnpathplot: no visible binding for global variable ‘p.adjust’
bnpathplot: no visible binding for global variable ‘gene_name’
bnpathplot: no visible global function definition for ‘prcomp’
bnpathplot: no visible global function definition for ‘cor’
bnpathplot: no visible binding for global variable ‘direction’
bnpathplot: no visible binding for global variable ‘label’
bnpathplot: no visible binding for global variable ‘value’
bnpathplot: no visible binding for global variable ‘name’
bnpathplot: no visible global function definition for ‘strength.viewer’
bnpathplot : <anonymous>: no visible binding for global variable
  ‘Description’
bnpathplotCustom: no visible binding for global variable ‘cell_line’
bnpathplotCustom: no visible binding for global variable ‘qvalue’
bnpathplotCustom: no visible binding for global variable ‘p.adjust’
bnpathplotCustom: no visible binding for global variable ‘gene_name’
bnpathplotCustom: no visible global function definition for ‘prcomp’
bnpathplotCustom: no visible global function definition for ‘cor’
bnpathplotCustom: no visible binding for global variable ‘direction’
bnpathplotCustom: no visible binding for global variable ‘label’
bnpathplotCustom: no visible binding for global variable ‘value’
bnpathplotCustom: no visible binding for global variable ‘name’
bnpathplotCustom : <anonymous>: no visible binding for global variable
  ‘Description’
bnpathtest: no visible binding for global variable ‘qvalue’
bnpathtest: no visible binding for global variable ‘p.adjust’
bnpathtest: no visible global function definition for ‘prcomp’
queryCpDistLs: no visible binding for global variable ‘level’
queryCpDistLs: no visible binding for global variable ‘freq’
queryCpDistLs: no visible binding for global variable ‘label’
queryCpDistLw: no visible binding for global variable ‘weights’
Undefined global functions or variables:
  ..count.. Description Pathway SYMBOL cell_line cls cor dependency
  depmap_id direction freq gene_name label level lineage name p.adjust
  prcomp qvalue strength.viewer value weights
Consider adding
  importFrom("stats", "cor", "p.adjust", "prcomp", "weights")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'bngeneplot.Rd':
  \examples lines wider than 100 characters:
     res <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, convertSymbol = TRUE, expRow = "ENSEMBL")

Rd file 'bngeneplotCustom.Rd':
  \examples lines wider than 100 characters:
     res <- bngeneplotCustom(results=exampleEaRes, exp=exampleGeneExp, chooseDir=TRUE, pathNum=1, glowEdgeNum=NULL, hub=3, R=40, fontFamily= ... [TRUNCATED]

Rd file 'bngenetest.Rd':
  \examples lines wider than 100 characters:
     res <- bngenetest(results = exampleEaRes, exp = exampleGeneExp, algo="hc", Rrange=seq(10, 30, 10), pathNum=1, scoreType="bge")

Rd file 'bnpathplotCustom.Rd':
  \examples lines wider than 100 characters:
     res <- bnpathplotCustom(results=exampleEaRes, exp=exampleGeneExp, fontFamily="sans", glowEdgeNum=3, hub=3)

Rd file 'bnpathtest.Rd':
  \examples lines wider than 100 characters:
     res <- bnpathtest(results = exampleEaRes, exp = exampleGeneExp, algo="hc", Rrange=seq(10, 30, 10), expRow = "ENSEMBL", scoreType="bge")

Rd file 'compareBNs.Rd':
  \examples lines wider than 100 characters:
     net1 <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, returnNet=TRUE)
     net2 <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, returnNet=TRUE)

Rd file 'queryCpDistLs.Rd':
  \examples lines wider than 100 characters:
     ## Not run: queryCpDistLs(fitted, candidate="Mitotic Spindle Checkpoint", evidences=c("TP53<0.5","TP53>0.5","TP53>0.8"), n=5000)

Rd file 'queryCpDistLw.Rd':
  \examples lines wider than 100 characters:
     ## Not run: queryCpDistLw(fitted, candidate="COL25A1", evidence = "Treatment", level=rownames(fitted$Treatment$prob))

These lines will be truncated in the PDF manual.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] 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 ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2477/CBNplot_20220301151746/CBNplot.Rcheck/00check.log’
for details.






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 BiocCheck('CBNplot_0.99.1.tar.gz')

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This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2477/CBNplot_20220301151746/CBNplot_0.99.1.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpDx8lAI/file3f163056f9aa/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1.0 to 4.2.0.
* Checking package size...
    * ERROR: Package Source tarball exceeds Bioconductor size
      requirement.
        Package Size: 77.7665 MB
        Size Requirement: 5.0000 MB
* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      'vignettes/CBNplot_basic_usage_cache/html/deg_4bcdba8ccbbef77784de899406629b26.rdb'
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      NetworkEnrichment
See http://bioconductor.org/developers/how-to/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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CBNplot...
* Checking coding practice...
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/bngeneplot.R (line 73, column 39)
        R/bngeneplot.R (line 95, column 31)
        R/bngeneplot.R (line 96, column 39)
        R/bngeneplot.R (line 101, column 31)
        R/bngeneplot.R (line 373, column 26)
        R/bngeneplot.R (line 374, column 27)
        R/bngeneplot.R (line 464, column 26)
        R/bngeneplotCustom.R (line 75, column 39)
        R/bngeneplotCustom.R (line 97, column 31)
        R/bnpathplot.R (line 78, column 38)
        R/bnpathplot.R (line 80, column 38)
        R/bnpathplot.R (line 86, column 27)
        R/bnpathplot.R (line 88, column 27)
        R/bnpathplot.R (line 119, column 39)
        R/bnpathplot.R (line 139, column 31)
        R/bnpathplot.R (line 198, column 13)
        R/bnpathplot.R (line 203, column 21)
        R/bnpathplot.R (line 224, column 34)
        R/bnpathplot.R (line 342, column 21)
        R/bnpathplot.R (line 343, column 30)
        R/bnpathplot.R (line 344, column 31)
        R/bnpathplot.R (line 351, column 21)
        R/bnpathplot.R (line 352, column 30)
        R/bnpathplot.R (line 353, column 31)
        R/bnpathplot.R (line 371, column 29)
        R/bnpathplot.R (line 373, column 29)
        R/bnpathplot.R (line 375, column 29)
        R/bnpathplotCustom.R (line 74, column 39)
        R/bnpathplotCustom.R (line 83, column 23)
        R/bnpathplotCustom.R (line 85, column 23)
        R/bnpathplotCustom.R (line 101, column 31)
        R/bnpathplotCustom.R (line 118, column 13)
        R/bnpathplotCustom.R (line 123, column 21)
        R/bnpathplotCustom.R (line 147, column 34)
        R/bnpathplotCustom.R (line 268, column 17)
        R/bnpathplotCustom.R (line 269, column 26)
        R/bnpathplotCustom.R (line 270, column 27)
        R/bnpathplotCustom.R (line 273, column 17)
        R/bnpathplotCustom.R (line 274, column 26)
        R/bnpathplotCustom.R (line 275, column 27)
        R/utilities.R (line 192, column 9)
        R/utilities.R (line 229, column 39)
        R/utilities.R (line 321, column 39)
        R/utilities.R (line 425, column 12)
        R/utilities.R (line 426, column 10)
        R/utilities.R (line 427, column 13)
        R/utilities.R (line 428, column 13)
        R/utilities.R (line 430, column 17)
        R/utilities.R (line 432, column 15)
        R/utilities.R (line 433, column 11)
        R/utilities.R (line 436, column 23)
        R/utilities.R (line 438, column 23)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
        suppressMessages() in R/bnpathplot.R (line 206, column 27)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 7 functions > 50 lines.
      The longest 5 functions are:
        bngeneplot() (R/bngeneplot.R, line 63): 463 lines
        bnpathplot() (R/bnpathplot.R, line 64): 395 lines
        bnpathplotCustom() (R/bnpathplotCustom.R, line 61): 320 lines
        bngeneplotCustom() (R/bngeneplotCustom.R, line 62): 298 lines
        bnpathtest() (R/utilities.R, line 226): 63 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      queryCpDistLs.Rd, queryCpDistLw.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      15% of man pages use one of these cases.
      Found in the following files:
        queryCpDistLs.Rd
        queryCpDistLw.Rd
    * NOTE: Use donttest{} instead of dontrun{}.
      Found in the following files:
        queryCpDistLs.Rd
        queryCpDistLw.Rd
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 355 lines (11%) are > 80 characters
      long.
    First 6 lines:
      R/bngeneplot.R:5 #' @param results the enrichment analysis result from ...
      R/bngeneplot.R:8 #' @param expSample candidate samples to be included i...
      R/bngeneplot.R:9 #' @param algo structure learning method used in boot....
      R/bngeneplot.R:10 #' @param algorithm.args parameters to pass to bnlear...
      R/bngeneplot.R:12 #' @param pathNum the pathway number (the number of r...
      R/bngeneplot.R:13 #' @param convertSymbol whether the label of resultin...
    * NOTE: Consider multiples of 4 spaces for line indents, 398
      lines(12%) are not.
    First 6 lines:
      R/bngeneplot.R:109                   axis.text = element_text(size=10),
      R/bngeneplot.R:110                   axis.title = element_text(size=12))
      R/bngeneplot.R:132           # rn <- clusterProfiler::bitr(rownames(pcs),
      R/bngeneplot.R:133           #                             fromType=exp...
      R/bngeneplot.R:134           #                             toType="SYMB...
      R/bngeneplot.R:135           #                             OrgDb=org.Hs...
    See http://bioconductor.org/developers/how-to/coding-style/
    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.


Summary:
ERROR count: 1
WARNING count: 1
NOTE count: 11
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir CBNplot_0.99.1.tar.gz'
>>>>>>> 

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