Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘octad/DESCRIPTION’ ... OK
* preparing ‘octad’:
* 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 ‘octad_0.99.56.tar.gz’

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 BiocCheckGitClone('octad')

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This is BiocCheckGitClone version 1.31.36. 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...
* Checking that provided CITATION file is correctly formatted...


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/2391/9080af8f59ae0e5134edef4f1b56f296fc4f1896/octad.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad/DESCRIPTION’ ... OK
* this is package ‘octad’ version ‘0.99.56’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma',
  'rhdf5', 'doParallel', 'foreach', 'Rfast', 'octad.db', 'httr',
  'ExperimentHub'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘octad’ can be installed ... [58s/58s] 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 ... NOTE
Package in Depends field not imported from: ‘doParallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [66s/66s] NOTE
computeCellLine : pick.out.cell.line: no visible binding for global
  variable ‘cell.line’
computeCellLine: no visible global function definition for ‘write.csv’
computeRefTissue: no visible binding for global variable ‘sample.type’
computeRefTissue: no visible binding for global variable ‘.’
computeRefTissue: no visible binding for global variable ‘sample.id’
computeRefTissue: no visible global function definition for ‘write.csv’
diffExp: no visible global function definition for ‘pData’
diffExp: no visible global function definition for ‘write.csv’
diffExp: no visible binding for global variable ‘identifier’
diffExp: no visible binding for global variable ‘case’
diffExp: no visible binding for global variable ‘control’
geneEnrich: no visible global function definition for ‘write.csv’
octadDrugEnrichment: no visible global function definition for ‘mcols’
octadDrugEnrichment: no visible global function definition for ‘query’
octadDrugEnrichment: no visible binding for global variable ‘title’
octadDrugEnrichment: no visible global function definition for
  ‘write.csv’
octadDrugEnrichment: no visible global function definition for ‘pdf’
octadDrugEnrichment: no visible global function definition for
  ‘dev.off’
octadDrugEnrichment: no visible global function definition for
  ‘read.csv2’
runsRGES: no visible binding for global variable ‘cell_id’
runsRGES: no visible binding for global variable ‘pert_iname’
runsRGES: no visible binding for global variable ‘pert_id’
runsRGES: no visible global function definition for ‘write.csv’
runsRGES: no visible binding for global variable ‘Symbol’
runsRGES: no visible binding for global variable ‘log2FoldChange’
runsRGES: no visible global function definition for ‘head’
runsRGES: no visible global function definition for ‘txtProgressBar’
runsRGES: no visible global function definition for ‘read.csv’
runsRGES: no visible binding for global variable ‘pert_dose’
runsRGES: no visible binding for global variable ‘pert_time’
runsRGES: no visible binding for global variable ‘id.x’
runsRGES: no visible binding for global variable ‘id.y’
runsRGES: no visible binding for global variable ‘pert_time.x’
runsRGES: no visible binding for global variable ‘pert_dose.x’
runsRGES: no visible binding for global variable ‘RGES’
runsRGES: no visible binding for global variable ‘ouput’
topLineEval: no visible binding for global variable ‘sRGES’
topLineEval: no visible binding for global variable ‘medIC50’
topLineEval: no visible binding for global variable ‘pert_iname’
topLineEval: no visible binding for global variable ‘medauc’
Undefined global functions or variables:
  . RGES Symbol case cell.line cell_id control dev.off head id.x id.y
  identifier log2FoldChange mcols medIC50 medauc ouput pData pdf
  pert_dose pert_dose.x pert_id pert_iname pert_time pert_time.x query
  read.csv read.csv2 sRGES sample.id sample.type title txtProgressBar
  write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "title")
  importFrom("utils", "head", "read.csv", "read.csv2", "txtProgressBar",
             "write.csv")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'computeCellLine.Rd':
  \usage lines wider than 90 characters:
      computeCellLine(case_id =case_id,expSet=NULL,LINCS_overlaps = TRUE, source='octad.small',file=NULL,output = FALSE,outputFolder='')

Rd file 'runsRGES.Rd':
  \examples lines wider than 100 characters:
     sRGES=runsRGES(dz_signature=res,max_gene_size=100,permutations=1000,output=FALSE,outputFolder = tempdir())

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 ... [357s/363s] ERROR
Running examples in ‘octad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: topLineEval
> ### Title: Evaluate cell lines
> ### Aliases: topLineEval
> ### Keywords: octadDrugEnrichment
> 
> ### ** Examples
> 
> #load example sRGES computed by runsRGES() function for HCC 
> #vs liver adjacent tissues on octad.small dataset
> data(sRGES_example)
> #Pick up cell lines
> topLineEval(topline = 'HEPG2',mysRGES = sRGES,outputFolder=tempdir())
Error in toupper(mysRGES$pert_iname) : object 'sRGES' not found
Calls: topLineEval -> toupper
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 ... OK
* DONE

Status: 1 ERROR, 5 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2391/9080af8f59ae0e5134edef4f1b56f296fc4f1896/octad.Rcheck/00check.log’
for details.





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 BiocCheck('octad_0.99.56.tar.gz')

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This is BiocCheck version 1.31.36. 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/2391/9080af8f59ae0e5134edef4f1b56f296fc4f1896/octad_0.99.56.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpB9nkSp/filee1396a659b5e/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...
* 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:
      Transcription, Sequencing, Epigenetics, Transcriptomics,
      Coverage, Normalization, Pathways, Preprocessing, Bayesian,
      Clustering, Regression, DNAMethylation, RNASeq, ChIPSeq,
      CellBiology, BiomedicalInformatics, FunctionalGenomics,
      SystemsBiology, ImmunoOncology, AlternativeSplicing,
      DifferentialExpression, DifferentialMethylation,
      DifferentialSplicing, BatchEffect, MultipleComparison,
      QualityControl, TimeCourse, ThirdPartyClient, DataImport, GUI
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 octad...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/octadDrugEnrichment.R (line 83, column 13)
        R/runsRGES_ultimate.R (line 55, column 29)
        R/runsRGES_ultimate.R (line 58, column 29)
        R/runsRGES_ultimate.R (line 72, column 31)
        R/runsRGES_ultimate.R (line 75, column 31)
        R/runsRGES_ultimate.R (line 180, column 6)
        R/runsRGES_ultimate.R (line 213, column 14)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        computeCellLine.R (line 36, column 68)
        computeCellLine.R (line 69, column 71)
        computeRefTissue.R (line 43, column 58)
        diffExp.R (line 40, column 68)
        diffExp.R (line 44, column 70)
        diffExp.R (line 88, column 54)
        geneEnrich.R (line 28, column 19)
        loadOctadCounts.R (line 12, column 65)
        loadOctadCounts.R (line 19, column 63)
        runsRGES_ultimate.R (line 200, column 16)
        runsRGES_ultimate.R (line 201, column 16)
        runsRGES_ultimate.R (line 243, column 21)
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        cat() in R/octadDrugEnrichment.R (line 22, column 9)
        cat() in R/octadDrugEnrichment.R (line 83, column 9)
        cat() in R/octadDrugEnrichment.R (line 91, column 5)
        cat() in R/octadDrugEnrichment.R (line 92, column 11)
        cat() in R/runsRGES_ultimate.R (line 17, column 1)
        cat() in R/runsRGES_ultimate.R (line 235, column 1)
        print() in R/topLineEval.R (line 129, column 1)
        print() in R/topLineEval.R (line 130, column 1)
        print() in R/topLineEval.R (line 131, column 1)
        print() in R/topLineEval.R (line 132, column 1)
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/computeCellLine.R (line 6, column 17)
        R/computeCellLine.R (line 12, column 20)
        R/computeCellLine.R (line 13, column 20)
        R/computeCellLine.R (line 14, column 20)
        R/computeCellLine.R (line 15, column 27)
        R/computeCellLine.R (line 16, column 54)
        R/computeCellLine.R (line 17, column 29)
        R/computeCellLine.R (line 18, column 23)
        R/computeCellLine.R (line 19, column 20)
        R/computeCellLine.R (line 20, column 10)
        R/computeCellLine.R (line 21, column 16)
        R/computeCellLine.R (line 23, column 28)
        R/computeCellLine.R (line 24, column 40)
        R/computeCellLine.R (line 29, column 21)
        R/computeCellLine.R (line 30, column 17)
        R/computeCellLine.R (line 31, column 21)
        R/computeCellLine.R (line 32, column 31)
        R/computeCellLine.R (line 33, column 31)
        R/computeCellLine.R (line 34, column 17)
        R/computeCellLine.R (line 36, column 21)
        R/computeCellLine.R (line 40, column 35)
        R/computeCellLine.R (line 41, column 28)
        R/computeCellLine.R (line 46, column 20)
        R/computeCellLine.R (line 49, column 22)
        R/computeCellLine.R (line 50, column 20)
        R/computeCellLine.R (line 52, column 44)
        R/computeCellLine.R (line 53, column 29)
        R/computeCellLine.R (line 56, column 21)
        R/computeCellLine.R (line 57, column 28)
        R/computeCellLine.R (line 58, column 5)
        R/computeCellLine.R (line 60, column 10)
        R/computeCellLine.R (line 61, column 11)
        R/computeCellLine.R (line 62, column 9)
        R/computeCellLine.R (line 63, column 31)
        R/computeCellLine.R (line 64, column 50)
        R/computeCellLine.R (line 65, column 23)
        R/computeCellLine.R (line 66, column 33)
        R/computeCellLine.R (line 67, column 18)
        R/computeCellLine.R (line 71, column 9)
        R/computeCellLine.R (line 76, column 17)
        R/computeRefTissue.R (line 14, column 15)
        R/computeRefTissue.R (line 15, column 16)
        R/computeRefTissue.R (line 18, column 24)
        R/computeRefTissue.R (line 19, column 30)
        R/computeRefTissue.R (line 20, column 27)
        R/computeRefTissue.R (line 21, column 27)
        R/computeRefTissue.R (line 23, column 35)
        R/computeRefTissue.R (line 28, column 26)
        R/computeRefTissue.R (line 30, column 10)
        R/computeRefTissue.R (line 43, column 30)
        R/computeRefTissue.R (line 45, column 16)
        R/computeRefTissue.R (line 47, column 20)
        R/computeRefTissue.R (line 48, column 15)
        R/diffExp.R (line 7, column 9)
        R/diffExp.R (line 18, column 12)
        R/diffExp.R (line 19, column 7)
        R/diffExp.R (line 20, column 11)
        R/diffExp.R (line 22, column 16)
        R/diffExp.R (line 30, column 21)
        R/diffExp.R (line 31, column 17)
        R/diffExp.R (line 32, column 21)
        R/diffExp.R (line 33, column 31)
        R/diffExp.R (line 34, column 31)
        R/diffExp.R (line 35, column 17)
        R/diffExp.R (line 36, column 23)
        R/diffExp.R (line 37, column 33)
        R/diffExp.R (line 38, column 33)
        R/diffExp.R (line 39, column 20)
        R/diffExp.R (line 41, column 16)
        R/diffExp.R (line 46, column 35)
        R/diffExp.R (line 47, column 23)
        R/diffExp.R (line 52, column 18)
        R/diffExp.R (line 54, column 18)
        R/diffExp.R (line 55, column 8)
        R/diffExp.R (line 56, column 8)
        R/diffExp.R (line 57, column 25)
        R/diffExp.R (line 58, column 30)
        R/diffExp.R (line 60, column 14)
        R/diffExp.R (line 61, column 8)
        R/diffExp.R (line 62, column 5)
        R/diffExp.R (line 67, column 16)
        R/diffExp.R (line 68, column 11)
        R/diffExp.R (line 69, column 11)
        R/diffExp.R (line 70, column 11)
        R/diffExp.R (line 71, column 11)
        R/diffExp.R (line 72, column 13)
        R/diffExp.R (line 73, column 13)
        R/diffExp.R (line 74, column 13)
        R/diffExp.R (line 75, column 11)
        R/diffExp.R (line 76, column 19)
        R/diffExp.R (line 81, column 14)
        R/diffExp.R (line 86, column 37)
        R/diffExp.R (line 87, column 17)
        R/diffExp.R (line 89, column 21)
        R/diffExp.R (line 93, column 21)
        R/diffExp.R (line 98, column 21)
        R/diffExp.R (line 100, column 29)
        R/diffExp.R (line 102, column 14)
        R/diffExp.R (line 103, column 16)
        R/diffExp.R (line 104, column 13)
        R/diffExp.R (line 105, column 24)
        R/diffExp.R (line 106, column 13)
        R/diffExp.R (line 112, column 40)
        R/diffExp.R (line 114, column 48)
        R/diffExp.R (line 116, column 48)
        R/diffExp.R (line 118, column 16)
        R/diffExp.R (line 120, column 24)
        R/diffExp.R (line 121, column 24)
        R/diffExp.R (line 123, column 16)
        R/diffExp.R (line 124, column 16)
        R/diffExp.R (line 125, column 16)
        R/diffExp.R (line 126, column 13)
        R/diffExp.R (line 128, column 13)
        R/diffExp.R (line 130, column 13)
        R/diffExp.R (line 131, column 23)
        R/diffExp.R (line 132, column 18)
        R/diffExp.R (line 133, column 24)
        R/diffExp.R (line 134, column 13)
        R/diffExp.R (line 138, column 11)
        R/diffExp.R (line 139, column 18)
        R/diffExp.R (line 140, column 14)
        R/diffExp.R (line 141, column 15)
        R/diffExp.R (line 142, column 16)
        R/diffExp.R (line 143, column 26)
        R/diffExp.R (line 144, column 22)
        R/diffExp.R (line 147, column 11)
        R/diffExp.R (line 148, column 14)
        R/diffExp.R (line 149, column 14)
        R/diffExp.R (line 150, column 14)
        R/diffExp.R (line 151, column 14)
        R/diffExp.R (line 152, column 12)
        R/diffExp.R (line 154, column 23)
        R/diffExp.R (line 155, column 23)
        R/diffExp.R (line 156, column 13)
        R/diffExp.R (line 157, column 23)
        R/diffExp.R (line 158, column 24)
        R/diffExp.R (line 161, column 25)
        R/diffExp.R (line 163, column 29)
        R/diffExp.R (line 164, column 28)
        R/diffExp.R (line 165, column 32)
        R/diffExp.R (line 166, column 30)
        R/diffExp.R (line 167, column 13)
        R/geneEnrich.R (line 3, column 11)
        R/geneEnrich.R (line 8, column 24)
        R/geneEnrich.R (line 9, column 9)
        R/geneEnrich.R (line 10, column 18)
        R/geneEnrich.R (line 15, column 16)
        R/geneEnrich.R (line 19, column 19)
        R/geneEnrich.R (line 20, column 19)
        R/geneEnrich.R (line 24, column 14)
        R/geneEnrich.R (line 28, column 18)
        R/geneEnrich.R (line 29, column 36)
        R/geneEnrich.R (line 34, column 20)
        R/geneEnrich.R (line 36, column 30)
        R/geneEnrich.R (line 37, column 26)
        R/geneEnrich.R (line 43, column 25)
        R/loadOctadCounts.R (line 8, column 13)
        R/loadOctadCounts.R (line 9, column 9)
        R/loadOctadCounts.R (line 12, column 18)
        R/loadOctadCounts.R (line 13, column 28)
        R/loadOctadCounts.R (line 14, column 28)
        R/loadOctadCounts.R (line 19, column 18)
        R/loadOctadCounts.R (line 20, column 28)
        R/loadOctadCounts.R (line 21, column 28)
        R/octadDrugEnrichment.R (line 6, column 21)
        R/octadDrugEnrichment.R (line 19, column 13)
        R/octadDrugEnrichment.R (line 20, column 18)
        R/octadDrugEnrichment.R (line 23, column 24)
        R/octadDrugEnrichment.R (line 28, column 18)
        R/octadDrugEnrichment.R (line 29, column 18)
        R/octadDrugEnrichment.R (line 30, column 25)
        R/octadDrugEnrichment.R (line 32, column 15)
        R/octadDrugEnrichment.R (line 33, column 11)
        R/octadDrugEnrichment.R (line 40, column 33)
        R/octadDrugEnrichment.R (line 41, column 22)
        R/octadDrugEnrichment.R (line 42, column 30)
        R/octadDrugEnrichment.R (line 43, column 29)
        R/octadDrugEnrichment.R (line 44, column 30)
        R/octadDrugEnrichment.R (line 50, column 39)
        R/octadDrugEnrichment.R (line 51, column 39)
        R/octadDrugEnrichment.R (line 52, column 30)
        R/octadDrugEnrichment.R (line 54, column 24)
        R/octadDrugEnrichment.R (line 57, column 24)
        R/octadDrugEnrichment.R (line 58, column 24)
        R/octadDrugEnrichment.R (line 60, column 29)
        R/octadDrugEnrichment.R (line 62, column 21)
        R/octadDrugEnrichment.R (line 65, column 21)
        R/octadDrugEnrichment.R (line 69, column 20)
        R/octadDrugEnrichment.R (line 70, column 20)
        R/octadDrugEnrichment.R (line 71, column 28)
        R/octadDrugEnrichment.R (line 80, column 22)
        R/octadDrugEnrichment.R (line 82, column 24)
        R/octadDrugEnrichment.R (line 84, column 19)
        R/octadDrugEnrichment.R (line 85, column 27)
        R/octadDrugEnrichment.R (line 86, column 24)
        R/octadDrugEnrichment.R (line 87, column 32)
        R/runsRGES_ultimate.R (line 18, column 11)
        R/runsRGES_ultimate.R (line 24, column 15)
        R/runsRGES_ultimate.R (line 40, column 20)
        R/runsRGES_ultimate.R (line 45, column 19)
        R/runsRGES_ultimate.R (line 46, column 17)
        R/runsRGES_ultimate.R (line 47, column 19)
        R/runsRGES_ultimate.R (line 48, column 25)
        R/runsRGES_ultimate.R (line 49, column 27)
        R/runsRGES_ultimate.R (line 108, column 32)
        R/runsRGES_ultimate.R (line 110, column 24)
        R/runsRGES_ultimate.R (line 115, column 14)
        R/runsRGES_ultimate.R (line 117, column 17)
        R/runsRGES_ultimate.R (line 119, column 18)
        R/runsRGES_ultimate.R (line 139, column 12)
        R/runsRGES_ultimate.R (line 141, column 14)
        R/runsRGES_ultimate.R (line 162, column 2)
        R/runsRGES_ultimate.R (line 163, column 12)
        R/runsRGES_ultimate.R (line 164, column 19)
        R/runsRGES_ultimate.R (line 165, column 13)
        R/runsRGES_ultimate.R (line 166, column 17)
        R/runsRGES_ultimate.R (line 167, column 15)
        R/runsRGES_ultimate.R (line 170, column 17)
        R/runsRGES_ultimate.R (line 173, column 19)
        R/runsRGES_ultimate.R (line 175, column 19)
        R/runsRGES_ultimate.R (line 208, column 14)
        R/topLineEval.R (line 9, column 13)
        R/topLineEval.R (line 16, column 17)
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* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 1 times)
        <<- in R/zzz.R (line 19, column 7)
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17
      times)
        suppressMessages() in R/computeCellLine.R (line 40, column 36)
        suppressMessages() in R/computeCellLine.R (line 49, column 23)
        suppressMessages() in R/computeCellLine.R (line 52, column 45)
        suppressMessages() in R/computeCellLine.R (line 57, column 29)
        suppressMessages() in R/computeRefTissue.R (line 14, column 16)
        suppressMessages() in R/computeRefTissue.R (line 18, column 25)
        suppressMessages() in R/diffExp.R (line 46, column 36)
        suppressMessages() in R/diffExp.R (line 161, column 26)
        suppressMessages() in R/octadDrugEnrichment.R (line 19, column
      14)
        suppressMessages() in R/octadDrugEnrichment.R (line 20, column
      19)
        suppressMessages() in R/octadDrugEnrichment.R (line 28, column
      19)
        suppressMessages() in R/runsRGES_ultimate.R (line 24, column
      16)
        suppressMessages() in R/runsRGES_ultimate.R (line 117, column
      18)
        suppressMessages() in R/runsRGES_ultimate.R (line 119, column
      19)
        suppressMessages() in R/runsRGES_ultimate.R (line 170, column
      18)
        suppressMessages() in R/topLineEval.R (line 22, column 44)
        suppressMessages() in R/topLineEval.R (line 38, column 47)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 7 functions > 50 lines.
      The longest 5 functions are:
        runsRGES() (R/runsRGES_ultimate.R, line 8): 231 lines
        diffExp() (R/diffExp.R, line 7): 164 lines
        topLineEval() (R/topLineEval.R, line 9): 128 lines
        octadDrugEnrichment() (R/octadDrugEnrichment.R, line 6): 90
      lines
        computeRefTissue() (R/computeRefTissue.R, line 6): 78 lines
* Checking man page documentation...
snapshotDate(): 2022-03-16
* 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; 245 lines (15%) are > 80 characters
      long.
    First 6 lines:
      R/computeCellLine.R:7 computeCellLine = function(case_id =case_id,expSe...
      R/computeCellLine.R:20 	correlation.matrix= cor(expr.of.samples[marker....
      R/computeCellLine.R:22 	cell.line.median.cor= apply(correlation.matrix,...
      R/computeCellLine.R:24 	p.value.vec= foreach::foreach(cell.line= setdif...
      R/computeCellLine.R:26 	p.value= wilcox.test(correlation.matrix[,best.c...
      R/computeCellLine.R:30 	list(cell.line.median.cor=cell.line.median.cor,...
    * NOTE: Consider 4 spaces instead of tabs; 338 lines (21%) contain
      tabs.
    First 6 lines:
      R/computeCellLine.R:10 	stop('Case ids vector input not found')
      R/computeCellLine.R:18 	marker.gene= intersect(rownames(expr.of.samples...
      R/computeCellLine.R:19 	marker.gene= intersect(rownames(expr.of.cell.li...
      R/computeCellLine.R:20 	correlation.matrix= cor(expr.of.samples[marker....
      R/computeCellLine.R:21 	correlation.matrix[is.na(correlation.matrix)]=0
      R/computeCellLine.R:22 	cell.line.median.cor= apply(correlation.matrix,...
    * NOTE: Consider multiples of 4 spaces for line indents, 75
      lines(5%) are not.
    First 6 lines:
      R/computeCellLine.R:16      #helper function by Ke
      R/computeCellLine.R:82   write.csv(correlation.dataframe, file = paste0...
      R/computeRefTissue.R:8                              method='varGenes',e...
      R/computeRefTissue.R:9                              outputFolder='',cor...
      R/octadDrugEnrichment.R:25    if (!dir.exists(enrichFolder.n)) {
      R/octadDrugEnrichment.R:31  	cmpdSets = cmpd_sets$cmpd.sets
    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: 0
WARNING count: 0
NOTE count: 13
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

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir octad_0.99.56.tar.gz'
>>>>>>> 

* installing *source* package ‘octad’ ...
** 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
snapshotDate(): 2022-03-16
** testing if installed package can be loaded from final location
snapshotDate(): 2022-03-16
** testing if installed package keeps a record of temporary installation path
* DONE (octad)