Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* preparing ‘EpiMix’:
* 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
* building ‘EpiMix_0.99.10.tar.gz’

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 BiocCheckGitClone('EpiMix')

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─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: EpiMix
─ PackageVersion: 0.99.10
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2558/588beb9a4c9062e10b53ca522e4536cbf399936a/EpiMix
─ 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...

─ 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 ‘/home/pkgbuild/packagebuilder/workers/jobs/2558/588beb9a4c9062e10b53ca522e4536cbf399936a/EpiMix.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* this is package ‘EpiMix’ 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 ‘EpiMix’ can be installed ... [39s/39s] 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 ... [53s/53s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'TCGA_Preprocess_GeneExpression.Rd':
  \examples lines wider than 100 characters:
      GEProcessedData <- TCGA_Preprocess_GeneExpression(CancerSite = 'OV',  MAdirectories = GEdirectories)

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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/38s] ERROR
Running examples in ‘EpiMix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GEO_Preprocess_GeneExpression
> ### Title: The GEO_Preprocess_GeneExpression function
> ### Aliases: GEO_Preprocess_GeneExpression
> ### Keywords: preprocess
> 
> ### ** Examples
> 
> {
+ data(mRNA.data)
+ data(LUAD.sample.annotation)
+ Preprocessed_Data <- GEO_Preprocess_GeneExpression(gene.expression.data = mRNA.data,
+                                                    sample.info = LUAD.sample.annotation,
+                                                    group.1 = 'Cancer',
+                                                    group.2 = 'Normal')
+ }
Removing duplicated transcripts...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%Error in match.names(clabs, names(xi)) : 
  names do not match previous names
Calls: GEO_Preprocess_GeneExpression ... removeDuplicatedGenes -> rbind -> rbind -> match.names
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘DT’
* 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: 1 ERROR, 2 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2558/588beb9a4c9062e10b53ca522e4536cbf399936a/EpiMix.Rcheck/00check.log’
for details.





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 BiocCheck('EpiMix_0.99.10.tar.gz')

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─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: EpiMix
─ PackageVersion: 0.99.10
─ sourceDir: /tmp/RtmpKkBJwe/file35e976bca223/EpiMix
─ installDir: /tmp/RtmpKkBJwe/file35e976369309c7
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2558/588beb9a4c9062e10b53ca522e4536cbf399936a/EpiMix.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* 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...
* 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 EpiMix...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.There are 28
      functions > 50 lines.
* Checking man page documentation...
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
    * NOTE: Usage of dontrun{} / donttest{} found in man page
      examples.15% of man pages use one of these cases.
* 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; 1628 lines (16%) are > 80
      characters long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1087 lines
      (11%) are not.
    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.

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 9 NOTES

See the EpiMix.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.