Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* preparing ‘Moonlight2R’:
* 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 ‘Moonlight2R_0.99.4.tar.gz’

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 BiocCheckGitClone('Moonlight2R')

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─ BiocCheckVersion: 1.37.8
─ BiocVersion: 3.18
─ Package: Moonlight2R
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2993/bc91a5ad5d3e9501b8bf5aed1e959c8641d09b8c/Moonlight2R
─ 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...
* Checking that provided CITATION file is correctly formatted...
    * NOTE: CITATION file might be not correctly formatted

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 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/2993/bc91a5ad5d3e9501b8bf5aed1e959c8641d09b8c/Moonlight2R.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ 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 ‘Moonlight2R’ 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 ... [13s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/14s] OK
* checking whether the package can be unloaded cleanly ... [13s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/14s] OK
* checking loading without being on the library search path ... [13s/14s] 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 ... [41s/47s] NOTE
DMA: no visible binding for global variable ‘Variant_Classification’
DMA: no visible binding for global variable ‘ID’
DMA: no visible binding for global variable ‘.’
DMA: no visible binding for global variable ‘Chromosome’
DMA: no visible binding for global variable ‘X1’
DMA: no visible binding for global variable ‘X2’
DMA: no visible binding for global variable ‘X3’
DMA: no visible binding for global variable ‘Annotation’
DMA: no visible binding for global variable ‘Annotation_Start’
DMA: no visible binding for global variable ‘Annotation_End’
DMA: no visible binding for global variable ‘Hugo_Symbol’
DMA: no visible binding for global variable
  ‘Moonlight_Oncogenic_Mediator’
DMA: no visible binding for global variable ‘CScape_Mut_Class’
DMA: no visible binding for global variable
  ‘Potential_Effect_on_Transcription’
DMA: no visible binding for global variable
  ‘Potential_Effect_on_Translation’
DMA: no visible binding for global variable
  ‘Potential_Effect_on_Protein’
DMA: no visible binding for global variable ‘CScape_Driver’
DMA: no visible binding for global variable ‘CScape_No_mutations’
DMA: no visible binding for global variable ‘Chr’
GLS : <anonymous>: no visible binding for global variable ‘pmid’
GLS : <anonymous>: no visible binding for global variable ‘doi’
GLS : <anonymous>: no visible binding for global variable ‘title’
GLS : <anonymous>: no visible binding for global variable ‘abstract’
GLS : <anonymous>: no visible binding for global variable ‘year’
GLS : <anonymous>: no visible binding for global variable ‘keywords’
GLS : <anonymous>: no visible binding for global variable ‘gene’
LiftMAF: no visible global function definition for ‘liftOver’
LiftMAF: no visible binding for global variable ‘start’
LiftMAF: no visible binding for global variable ‘end’
LiftMAF: no visible binding for global variable ‘seqnames’
LiftMAF: no visible binding for global variable ‘strand’
LiftMAF: no visible binding for global variable ‘group’
LiftMAF: no visible binding for global variable ‘group_name’
LiftMAF: no visible binding for global variable ‘width’
MAFtoCscape: no visible binding for global variable ‘Variant_Type’
MAFtoCscape: no visible binding for global variable ‘Chromosome’
MAFtoCscape: no visible binding for global variable ‘Start_Position’
MAFtoCscape: no visible binding for global variable ‘Reference_Allele’
MAFtoCscape: no visible binding for global variable ‘Tumor_Seq_Allele1’
MAFtoCscape: no visible binding for global variable ‘Tumor_Seq_Allele2’
MAFtoCscape: no visible binding for global variable ‘Chr’
MAFtoCscape: no visible binding for global variable ‘Mutant’
PRAtoTibble: no visible binding for global variable ‘Hugo_Symbol’
PRAtoTibble: no visible binding for global variable ‘value’
RunCscape_somatic: no visible binding for global variable ‘Ranges’
RunCscape_somatic: no visible binding for global variable
  ‘Start_Position’
RunCscape_somatic: no visible binding for global variable
  ‘Reference_Allele’
RunCscape_somatic: no visible binding for global variable ‘Mutant’
RunCscape_somatic: no visible binding for global variable ‘file_coding’
RunCscape_somatic: no visible binding for global variable
  ‘file_noncoding’
RunCscape_somatic: no visible binding for global variable ‘Mydata’
RunCscape_somatic: no visible binding for global variable ‘Remark’
plotDMA: no visible binding for global variable ‘Hugo_Symbol’
plotDMA: no visible binding for global variable ‘logFC’
plotDMA: no visible binding for global variable ‘CScape_Driver’
plotDMA: no visible binding for global variable ‘CScape_Passenger’
plotDMA: no visible binding for global variable ‘CScape_Unclassified’
plotDMA: no visible binding for global variable
  ‘Moonlight_Oncogenic_Mediator’
plotDMA: no visible binding for global variable ‘Mutation_type’
plotDMA: no visible binding for global variable ‘Count’
plotDMA: no visible binding for global variable ‘Total_Mutations’
plotDMA: no visible binding for global variable ‘gr’
plotDMA: no visible binding for global variable ‘heatmaps’
plotDMA: no visible binding for global variable ‘First_gene’
plotHeatmap: no visible binding for global variable
  ‘Moonlight_Oncogenic_Mediator’
plotHeatmap: no visible binding for global variable ‘Mutation_type’
plotHeatmap: no visible binding for global variable ‘Hugo_Symbol’
plotHeatmap: no visible binding for global variable ‘Count’
plotHeatmap: no visible binding for global variable ‘Total_Mutations’
plotHeatmap: no visible binding for global variable ‘logFC’
plotMoonlight: no visible binding for global variable ‘Hugo_Symbol’
plotMoonlight: no visible binding for global variable
  ‘Moonlight_gene_z_score’
plotMoonlight: no visible binding for global variable ‘logFC’
plotMoonlight: no visible binding for global variable
  ‘Biological_Process’
plotMoonlight: no visible binding for global variable ‘Genes’
plotMoonlight: no visible binding for global variable ‘Total_Mutations’
plotMoonlight: no visible binding for global variable ‘CScape_Driver’
plotMoonlight: no visible binding for global variable
  ‘Moonlight_Oncogenic_Mediator’
plotMoonlight: no visible global function definition for ‘head’
plotMoonlight: no visible binding for global variable ‘Moonlight_score’
tabix_func: no visible binding for global variable ‘.’
tabix_func: no visible binding for global variable ‘V4’
tabix_func: no visible binding for global variable ‘V5’
Undefined global functions or variables:
  . Annotation Annotation_End Annotation_Start Biological_Process
  CScape_Driver CScape_Mut_Class CScape_No_mutations CScape_Passenger
  CScape_Unclassified Chr Chromosome Count First_gene Genes Hugo_Symbol
  ID Moonlight_Oncogenic_Mediator Moonlight_gene_z_score
  Moonlight_score Mutant Mutation_type Mydata
  Potential_Effect_on_Protein Potential_Effect_on_Transcription
  Potential_Effect_on_Translation Ranges Reference_Allele Remark
  Start_Position Total_Mutations Tumor_Seq_Allele1 Tumor_Seq_Allele2 V4
  V5 Variant_Classification Variant_Type X1 X2 X3 abstract doi end
  file_coding file_noncoding gene gr group group_name head heatmaps
  keywords liftOver logFC pmid seqnames start strand title value width
  year
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "end", "start")
  importFrom("utils", "head")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘Moonlight2R/R/DMA.R’:
  data("LOC_transcription")
  data("LOC_translation")
  data("LOC_protein")
File ‘Moonlight2R/R/FEA.R’:
  data("DiseaseList")
  data("EAGenes")
File ‘Moonlight2R/R/PRA.R’:
  data("tabGrowBlock")
  data("knownDriverGenes")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GLS.Rd':
  \examples lines wider than 100 characters:
                    query_string = "AND cancer AND driver AND '1980/01/01'[Date - Publication] : '2023/01/01'[Date - Publication]")

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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/64s] OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
GLS        2.984  1.233   8.526
getDataGEO 1.183  0.481   6.019
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [33s/36s]
 [33s/36s] 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 ... [4s/4s] OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2993/bc91a5ad5d3e9501b8bf5aed1e959c8641d09b8c/Moonlight2R.Rcheck/00check.log’
for details.






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 BiocCheck('Moonlight2R_0.99.4.tar.gz')

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─ BiocCheckVersion: 1.37.8
─ BiocVersion: 3.18
─ Package: Moonlight2R
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp8SFvb5/file37084ed58c36/Moonlight2R
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp8SFvb5/file3708384fddb0
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2993/bc91a5ad5d3e9501b8bf5aed1e959c8641d09b8c/Moonlight2R.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* 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 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      DriverMutation, SomaticMutation
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
    * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for recommeded fields in DESCRIPTION...
* 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 Moonlight2R...
* 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
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 11 functions greater than 50 lines.
* Checking man page documentation...

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 6% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* 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; 387 lines (8%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 11 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 692 lines
      (14%) 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 | 15 NOTES

See the Moonlight2R.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 Moonlight2R_0.99.4.tar.gz'
>>>>>>> 

* installing *source* package ‘Moonlight2R’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (Moonlight2R)