Multiple platform build/check report for BioC 3.14 - CHECK results for bigmelon on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: bigmelon

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bigmelon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bigmelon_1.20.0.tar.gz

StartedAt: 2022-04-12 16:10:25 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 16:20:02 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 576.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: bigmelon.Rcheck

Warnings: 2

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bigmelon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bigmelon_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/bigmelon.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bigmelon/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bigmelon' version '1.20.0'
* 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 whether package 'bigmelon' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'bumphunter:::greaterOrEqual' 'minfi:::pickCompProbes'
  'minfi:::projectCellType' 'wateRmelon:::.impose'
  'wateRmelon:::.normalizeQuantiles2'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bumphunterEngine.gdsn: no visible binding for global variable
  'locfitByCluster'
bumphunterEngine.gdsn: no visible global function definition for
  'getDoParRegistered'
bumphunterEngine.gdsn: no visible global function definition for
  'registerDoSEQ'
bumphunterEngine.gdsn: no visible global function definition for
  'getDoParWorkers'
bumphunterEngine.gdsn: no visible global function definition for
  'getDoParName'
bumphunterEngine.gdsn: no visible global function definition for
  'getDoParVersion'
bumphunterEngine.gdsn: no visible global function definition for
  'smoother'
bumphunterEngine.gdsn: no visible global function definition for
  'regionFinder'
bumphunterEngine.gdsn: no visible global function definition for
  '%dorng%'
bumphunterEngine.gdsn: no visible global function definition for
  'foreach'
bumphunterEngine.gdsn: no visible global function definition for 'iter'
bumphunterEngine.gdsn: no visible binding for global variable
  'regionFinder'
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for '%dorng%'
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for 'foreach'
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for 'iter'
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for '%dorng%'
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for 'foreach'
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for 'iter'
es2gds: no visible global function definition for 'colData'
estimateCellCounts.gds: no visible global function definition for
  'colData'
Undefined global functions or variables:
  %dorng% colData foreach getDoParName getDoParRegistered
  getDoParVersion getDoParWorkers iter locfitByCluster regionFinder
  registerDoSEQ smoother
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'iadd':
iadd
  Code: function(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL,
                 ...)
  Docs: function(bar, gds, n = TRUE, force = FALSE, target_cpgs = NULL,
                 ...)
  Mismatches in argument default values:
    Name: 'force' Code: TRUE Docs: FALSE
iadd2
  Code: function(path, gds, chunksize = NULL, force = TRUE, ...)
  Docs: function(path, gds, chunksize = NULL, force = FALSE, ...)
  Mismatches in argument default values:
    Name: 'force' Code: TRUE Docs: FALSE

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'iadd'
  'force' 'barcodes'
Documented arguments not in \usage in documentation object 'iadd':
  'Force'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
iadd 33.32   1.83   35.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
iadd 32.86   1.97   35.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/bigmelon.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/bigmelon_1.20.0.tar.gz && rm -rf bigmelon.buildbin-libdir && mkdir bigmelon.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bigmelon.buildbin-libdir bigmelon_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL bigmelon_1.20.0.zip && rm bigmelon_1.20.0.tar.gz bigmelon_1.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 93  683k   93  640k    0     0  1310k      0 --:--:-- --:--:-- --:--:-- 1309k
100  683k  100  683k    0     0  1390k      0 --:--:-- --:--:-- --:--:-- 1391k

install for i386

* installing *source* package 'bigmelon' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
Creating a new generic function for 'fot' in package 'bigmelon'
** help
*** installing help indices
  converting help for package 'bigmelon'
    finding HTML links ... done
    GEOtoGDS                                html  
    app2gds                                 html  
    backupGdsn                              html  
    bigmelon-accessors                      html  
    bigmelon-internal                       html  
    bigmelon-normalization                  html  
    finding level-2 HTML links ... done

    bigmelon-package                        html  
    bumphunterGdsn                          html  
    cantaloupe                              html  
    combogds                                html  
    ecc                                     html  
    es2gds                                  html  
    finalreport2gds                         html  
    gds2mlumi                               html  
    getquantilesandranks                    html  
    iadd                                    html  
    pfiltergds                              html  
    prcompgdsn                              html  
    pwodgdsn                                html  
    rankednorm                              html  
    redirect                                html  
    wm-port                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'bigmelon' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'bigmelon' as bigmelon_1.20.0.zip
* DONE (bigmelon)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'bigmelon' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("bigmelon")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows



Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

locfit 1.5-9.5 	 2022-03-01
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'

Attaching package: 'lumi'

The following objects are masked from 'package:methylumi':

    estimateM, getHistory


Attaching package: 'bigmelon'

The following object is masked from 'package:wateRmelon':

    fot

t8.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t9.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t2.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
appending to C:\Users\biocbuild\bbs-3.14-bioc\meat\bigmelon.Rcheck\tests_i386\t2.gds
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
t3.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t4.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t0.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t5.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t7.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t6.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.


RUNIT TEST PROTOCOL -- Tue Apr 12 16:19:35 2022 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bigmelon RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
  15.07    1.71   17.29


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("bigmelon")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows



Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

locfit 1.5-9.5 	 2022-03-01
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'

Attaching package: 'lumi'

The following objects are masked from 'package:methylumi':

    estimateM, getHistory


Attaching package: 'bigmelon'

The following object is masked from 'package:wateRmelon':

    fot

t8.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t9.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t2.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
appending to C:\Users\biocbuild\bbs-3.14-bioc\meat\bigmelon.Rcheck\tests_x64\t2.gds
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
t3.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t4.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t0.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t5.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t7.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t6.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.


RUNIT TEST PROTOCOL -- Tue Apr 12 16:19:54 2022 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bigmelon RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
  17.37    0.90   18.43

name	user	system	elapsed
GEOtoGDS	0	0	0
app2gds	0.48	0.06	1.76
backupGdsn	0.37	0.01	0.39
bigmelon-accessors	0.33	0.02	0.34
bigmelon-internal	0.28	0.03	0.39
bigmelon-normalization	3.97	0.20	4.25
combogds	0.59	0.03	0.64
es2gds	0.32	0.00	0.31
finalreport2gds	0	0	0
gds2mlumi	0.59	0.03	0.63
getquantilesandranks	0.30	0.14	0.44
iadd	33.32	1.83	35.36
pfiltergds	0.55	0.08	0.65
prcompgdsn	0.31	0.08	0.39
pwodgdsn	0.74	0.12	0.86
rankednorm	0.28	0.07	0.35
redirect	0.42	0.04	0.46

name	user	system	elapsed
GEOtoGDS	0	0	0
app2gds	0.55	0.04	0.78
backupGdsn	0.31	0.04	0.34
bigmelon-accessors	0.35	0.03	0.71
bigmelon-internal	0.31	0.03	0.64
bigmelon-normalization	3.57	0.22	3.91
combogds	0.52	0.09	0.84
es2gds	0.31	0.02	0.44
finalreport2gds	0	0	0
gds2mlumi	0.58	0.06	0.65
getquantilesandranks	0.39	0.01	0.56
iadd	32.86	1.97	35.61
pfiltergds	0.48	0.00	2.05
prcompgdsn	0.30	0.07	0.41
pwodgdsn	0.67	0.04	0.81
rankednorm	0.20	0.06	0.27
redirect	0.17	0.05	0.21

CHECK results for bigmelon on tokay2

Summary

Command output

Installation output

Tests output

Example timings