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_0.99.44.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 ‘/home/pkgbuild/packagebuilder/workers/jobs/2391/8fcc943ab898f243ba11dd0efd00c760d6517d1f/octad.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad/DESCRIPTION’ ... OK
* this is package ‘octad’ version ‘0.99.44’
* 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 ... [35s/35s] 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 ... [36s/37s] 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’
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 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 'octadDrugEnrichment.Rd':
  \examples lines wider than 100 characters:
     #load example sRGES computed by runsRGES() function for HCC vs liver adjacent tissues on octad.small dataset

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 ... WARNING
Codoc mismatches from documentation object 'runsRGES':
runsRGES
  Code: function(dz_signature = NULL, choose_fda_drugs = FALSE,
                 max_gene_size = 500, cells = NULL, outputFolder = "",
                 weight_cell_line = NULL, permutations = 10000)
  Docs: function(dz_signature = NULL, choose_fda_drugs = FALSE,
                 max_gene_size = 500, cells = NULL, outputFolder =
                 NULL, weight_cell_line = NULL, permutations = 10000)
  Mismatches in argument default values:
    Name: 'outputFolder' Code: "" Docs: NULL

Codoc mismatches from documentation object 'topLineEval':
topLineEval
  Code: function(topline = c(""), mysRGES = NULL, outputFolder = "")
  Docs: function(topline, mysRGES)
  Argument names in code not in docs:
    outputFolder
  Mismatches in argument default values:
    Name: 'topline' Code: c("") Docs: 
    Name: 'mysRGES' Code: NULL Docs: 

* 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 ... [88s/97s] ERROR
Running examples in ‘octad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: octadDrugEnrichment
> ### Title: Compute Drug enrichment
> ### Aliases: octadDrugEnrichment
> ### Keywords: octadDrugEnrichment
> 
> ### ** Examples
> 
> #load example sRGES computed by runsRGES() function for HCC vs liver adjacent tissues on octad.small dataset
> sRGES=ExperimentHub()[["EH7279"]]
snapshotDate(): 2022-03-16
see ?octad.db and browseVignettes('octad.db') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
> #run drug enrichment 
> octadDrugEnrichment(sRGES = sRGES, target_type = c('chembl_targets'))
Running enrichment for chembl_targets 
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
Error in `rownames<-`(`*tmp*`, value = names(geneSets)) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: octadDrugEnrichment ... <Anonymous> -> .local -> .gsva -> ssgsea -> rownames<-
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, 1 WARNING, 5 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2391/8fcc943ab898f243ba11dd0efd00c760d6517d1f/octad.Rcheck/00check.log’
for details.





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 BiocCheck('octad_0.99.44.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 '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2391/8fcc943ab898f243ba11dd0efd00c760d6517d1f/octad_0.99.44.tar.gz" "/tmp/RtmpVdknXa/file2c727970a32935/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 72, column 13)
        R/runsRGES_ultimate.R (line 49, column 29)
        R/runsRGES_ultimate.R (line 52, column 29)
        R/runsRGES_ultimate.R (line 66, column 31)
        R/runsRGES_ultimate.R (line 69, column 31)
        R/runsRGES_ultimate.R (line 174, column 6)
        R/runsRGES_ultimate.R (line 205, 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 52, 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 193, column 16)
        runsRGES_ultimate.R (line 194, column 16)
        runsRGES_ultimate.R (line 234, column 21)
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        cat() in R/octadDrugEnrichment.R (line 21, column 9)
        cat() in R/octadDrugEnrichment.R (line 72, column 9)
        cat() in R/octadDrugEnrichment.R (line 80, column 5)
        cat() in R/octadDrugEnrichment.R (line 81, column 11)
        cat() in R/runsRGES_ultimate.R (line 16, column 1)
        cat() in R/runsRGES_ultimate.R (line 223, 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 72, column 9)
        R/computeCellLine.R (line 76, column 17)
        R/computeRefTissue.R (line 23, column 15)
        R/computeRefTissue.R (line 24, column 16)
        R/computeRefTissue.R (line 27, column 24)
        R/computeRefTissue.R (line 28, column 30)
        R/computeRefTissue.R (line 29, column 27)
        R/computeRefTissue.R (line 30, column 27)
        R/computeRefTissue.R (line 32, column 35)
        R/computeRefTissue.R (line 37, column 26)
        R/computeRefTissue.R (line 39, column 10)
        R/computeRefTissue.R (line 52, column 30)
        R/computeRefTissue.R (line 54, column 16)
        R/computeRefTissue.R (line 56, column 20)
        R/computeRefTissue.R (line 57, 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 79, column 14)
        R/diffExp.R (line 84, column 37)
        R/diffExp.R (line 85, column 17)
        R/diffExp.R (line 87, column 21)
        R/diffExp.R (line 91, column 21)
        R/diffExp.R (line 96, column 21)
        R/diffExp.R (line 98, column 29)
        R/diffExp.R (line 100, column 14)
        R/diffExp.R (line 101, column 16)
        R/diffExp.R (line 102, column 13)
        R/diffExp.R (line 103, column 24)
        R/diffExp.R (line 104, column 13)
        R/diffExp.R (line 110, column 40)
        R/diffExp.R (line 112, column 48)
        R/diffExp.R (line 114, column 48)
        R/diffExp.R (line 116, column 16)
        R/diffExp.R (line 118, column 24)
        R/diffExp.R (line 119, column 24)
        R/diffExp.R (line 121, column 16)
        R/diffExp.R (line 122, column 16)
        R/diffExp.R (line 123, column 16)
        R/diffExp.R (line 124, column 13)
        R/diffExp.R (line 126, column 13)
        R/diffExp.R (line 128, column 13)
        R/diffExp.R (line 129, column 23)
        R/diffExp.R (line 130, column 18)
        R/diffExp.R (line 131, column 24)
        R/diffExp.R (line 132, column 13)
        R/diffExp.R (line 136, column 11)
        R/diffExp.R (line 137, column 18)
        R/diffExp.R (line 138, column 14)
        R/diffExp.R (line 139, column 15)
        R/diffExp.R (line 140, column 16)
        R/diffExp.R (line 141, column 26)
        R/diffExp.R (line 142, column 22)
        R/diffExp.R (line 145, column 11)
        R/diffExp.R (line 146, column 14)
        R/diffExp.R (line 147, column 14)
        R/diffExp.R (line 148, column 14)
        R/diffExp.R (line 149, column 14)
        R/diffExp.R (line 150, column 12)
        R/diffExp.R (line 152, column 23)
        R/diffExp.R (line 153, column 23)
        R/diffExp.R (line 154, column 13)
        R/diffExp.R (line 155, column 23)
        R/diffExp.R (line 156, column 24)
        R/diffExp.R (line 159, column 25)
        R/diffExp.R (line 161, column 29)
        R/diffExp.R (line 162, column 28)
        R/diffExp.R (line 163, column 32)
        R/diffExp.R (line 164, column 30)
        R/diffExp.R (line 165, 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 11)
        R/octadDrugEnrichment.R (line 22, column 24)
        R/octadDrugEnrichment.R (line 27, column 18)
        R/octadDrugEnrichment.R (line 29, column 18)
        R/octadDrugEnrichment.R (line 30, column 25)
        R/octadDrugEnrichment.R (line 31, column 26)
        R/octadDrugEnrichment.R (line 34, column 15)
        R/octadDrugEnrichment.R (line 35, column 11)
        R/octadDrugEnrichment.R (line 36, column 21)
        R/octadDrugEnrichment.R (line 37, column 18)
        R/octadDrugEnrichment.R (line 38, column 18)
        R/octadDrugEnrichment.R (line 39, column 28)
        R/octadDrugEnrichment.R (line 40, column 27)
        R/octadDrugEnrichment.R (line 41, column 18)
        R/octadDrugEnrichment.R (line 43, column 12)
        R/octadDrugEnrichment.R (line 46, column 12)
        R/octadDrugEnrichment.R (line 47, column 12)
        R/octadDrugEnrichment.R (line 49, column 17)
        R/octadDrugEnrichment.R (line 51, column 21)
        R/octadDrugEnrichment.R (line 54, column 21)
        R/octadDrugEnrichment.R (line 58, column 20)
        R/octadDrugEnrichment.R (line 59, column 20)
        R/octadDrugEnrichment.R (line 60, column 28)
        R/octadDrugEnrichment.R (line 69, column 22)
        R/octadDrugEnrichment.R (line 71, column 24)
        R/octadDrugEnrichment.R (line 73, column 19)
        R/octadDrugEnrichment.R (line 74, column 27)
        R/octadDrugEnrichment.R (line 75, column 24)
        R/octadDrugEnrichment.R (line 76, column 32)
        R/runsRGES_ultimate.R (line 17, column 11)
        R/runsRGES_ultimate.R (line 18, column 15)
        R/runsRGES_ultimate.R (line 34, column 20)
        R/runsRGES_ultimate.R (line 39, column 19)
        R/runsRGES_ultimate.R (line 40, column 17)
        R/runsRGES_ultimate.R (line 41, column 19)
        R/runsRGES_ultimate.R (line 42, column 25)
        R/runsRGES_ultimate.R (line 43, column 27)
        R/runsRGES_ultimate.R (line 102, column 32)
        R/runsRGES_ultimate.R (line 104, column 24)
        R/runsRGES_ultimate.R (line 109, column 14)
        R/runsRGES_ultimate.R (line 111, column 17)
        R/runsRGES_ultimate.R (line 113, column 18)
        R/runsRGES_ultimate.R (line 135, column 12)
        R/runsRGES_ultimate.R (line 137, column 14)
        R/runsRGES_ultimate.R (line 156, column 2)
        R/runsRGES_ultimate.R (line 157, column 12)
        R/runsRGES_ultimate.R (line 158, column 19)
        R/runsRGES_ultimate.R (line 159, column 13)
        R/runsRGES_ultimate.R (line 160, column 17)
        R/runsRGES_ultimate.R (line 161, column 15)
        R/runsRGES_ultimate.R (line 164, column 17)
        R/runsRGES_ultimate.R (line 167, column 19)
        R/runsRGES_ultimate.R (line 169, column 19)
        R/runsRGES_ultimate.R (line 200, column 14)
        R/topLineEval.R (line 9, column 13)
        R/topLineEval.R (line 16, column 17)
        R/topLineEval.R (line 17, column 22)
        R/topLineEval.R (line 21, column 20)
        R/topLineEval.R (line 22, column 13)
        R/topLineEval.R (line 24, column 23)
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        R/topLineEval.R (line 28, column 12)
        R/topLineEval.R (line 29, column 10)
        R/topLineEval.R (line 30, column 13)
        R/topLineEval.R (line 31, column 21)
        R/topLineEval.R (line 32, column 29)
        R/topLineEval.R (line 33, column 27)
        R/topLineEval.R (line 34, column 28)
        R/topLineEval.R (line 35, column 29)
        R/topLineEval.R (line 37, column 22)
        R/topLineEval.R (line 38, column 16)
        R/topLineEval.R (line 40, column 22)
        R/topLineEval.R (line 41, column 22)
        R/topLineEval.R (line 42, column 22)
        R/topLineEval.R (line 44, column 11)
        R/topLineEval.R (line 45, column 9)
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        R/topLineEval.R (line 50, column 26)
        R/topLineEval.R (line 51, column 25)
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        R/topLineEval.R (line 58, column 8)
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        R/topLineEval.R (line 60, column 10)
        R/topLineEval.R (line 61, column 12)
        R/topLineEval.R (line 62, column 9)
        R/topLineEval.R (line 63, column 26)
        R/topLineEval.R (line 64, column 26)
        R/topLineEval.R (line 65, column 19)
        R/topLineEval.R (line 66, column 14)
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        R/topLineEval.R (line 69, column 7)
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        R/topLineEval.R (line 73, column 3)
        R/topLineEval.R (line 81, column 4)
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        R/topLineEval.R (line 86, column 18)
        R/topLineEval.R (line 88, column 18)
        R/topLineEval.R (line 93, column 9)
        R/topLineEval.R (line 94, column 13)
        R/topLineEval.R (line 95, column 27)
        R/topLineEval.R (line 96, column 27)
        R/topLineEval.R (line 97, column 19)
        R/topLineEval.R (line 98, column 9)
        R/topLineEval.R (line 99, column 7)
        R/topLineEval.R (line 100, column 14)
        R/topLineEval.R (line 101, column 14)
        R/topLineEval.R (line 102, column 14)
        R/topLineEval.R (line 103, column 7)
        R/topLineEval.R (line 104, column 7)
        R/topLineEval.R (line 105, column 7)
        R/topLineEval.R (line 106, column 3)
        R/topLineEval.R (line 115, column 4)
        R/topLineEval.R (line 116, column 10)
        R/topLineEval.R (line 119, column 18)
        R/topLineEval.R (line 121, column 18)
        R/topLineEval.R (line 126, column 5)
* 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 23, column 16)
        suppressMessages() in R/computeRefTissue.R (line 27, column 25)
        suppressMessages() in R/diffExp.R (line 46, column 36)
        suppressMessages() in R/diffExp.R (line 159, column 26)
        suppressMessages() in R/octadDrugEnrichment.R (line 19, column
      12)
        suppressMessages() in R/octadDrugEnrichment.R (line 27, column
      19)
        suppressMessages() in R/octadDrugEnrichment.R (line 31, column
      27)
        suppressMessages() in R/runsRGES_ultimate.R (line 18, column
      16)
        suppressMessages() in R/runsRGES_ultimate.R (line 111, column
      18)
        suppressMessages() in R/runsRGES_ultimate.R (line 113, column
      19)
        suppressMessages() in R/runsRGES_ultimate.R (line 164, 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): 219 lines
        diffExp() (R/diffExp.R, line 7): 162 lines
        topLineEval() (R/topLineEval.R, line 9): 128 lines
        computeRefTissue() (R/computeRefTissue.R, line 6): 87 lines
        octadDrugEnrichment() (R/octadDrugEnrichment.R, line 6): 79
      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; 238 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; 307 lines (19%) 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, 79
      lines(5%) are not.
    First 6 lines:
      R/computeCellLine.R:16      #helper function by Ke
      R/computeRefTissue.R:8                              adjacent=FALSE,
      R/computeRefTissue.R:9                              source='octad',n_va...
      R/computeRefTissue.R:10                              method='varGenes',...
      R/computeRefTissue.R:11                              expSet=NULL,
      R/computeRefTissue.R:12                              #site_selection = ...
    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