##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings bigmelon_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/bigmelon.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘bigmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigmelon’ version ‘1.25.1’
* 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 ‘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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    1.1.14 Added gdsfmt method for estimating Cell Counts, added an experimental normalisation methodology, which involves storing raw intensities as ranks and performing re-ranking steps down-stream with computed quantiles. 
  Cannot process chunk/lines:
    0.99.4  Commit to Github from svn
  Cannot process chunk/lines:
    0.1.2	app2gds simple data appending function
* 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 startup messages can be suppressed ... NOTE
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
iadd 29.871  1.036   31.02
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bigmelon.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/bigmelon.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL bigmelon
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* 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
** 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
* DONE (bigmelon)

R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, aperm, 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: '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 1.5-9.7 	 2023-01-02
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 /home/biocbuild/bbs-3.17-bioc/meat/bigmelon.Rcheck/tests/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 11 18:55:11 2023 
*********************************************** 
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 
 16.355   0.951  17.297