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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 164/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigmelon 1.31.0  (landing page)
Leonard C. Schalkwyk
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/bigmelon
git_branch: devel
git_last_commit: bdfe364
git_last_commit_date: 2024-04-30 10:53:41 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for bigmelon on kjohnson1

To the developers/maintainers of the bigmelon package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bigmelon.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: bigmelon
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bigmelon_1.31.0.tar.gz
StartedAt: 2024-06-10 12:52:30 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 13:00:09 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 459.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: bigmelon.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bigmelon_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/bigmelon.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bigmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigmelon’ version ‘1.31.0’
* 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 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 ... OK
* checking code 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 whether 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’
idats2gds: no visible binding for global variable ‘ChipType’
Undefined global functions or variables:
  %dorng% ChipType 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 ... WARNING
Undocumented code objects:
  ‘dim.gdsn.class’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'iadd.Rd':
iadd
  Code: function(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL,
                 idatpath = NULL, ...)
  Docs: function(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL,
                 ...)
  Argument names in code not in docs:
    idatpath
  Mismatches in argument names:
    Position: 6 Code: idatpath Docs: ...

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'dim.gds.class.Rd'
  ‘gfile’ ‘v’

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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
iadd 35.458  1.604  37.181
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/bigmelon.Rcheck/00check.log’
for details.


Installation output

bigmelon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bigmelon
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)

Tests output

bigmelon.Rcheck/tests/runTests.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, 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 object is masked from 'package:utils':

    findMatches

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 1.5-9.9 	 2024-03-01
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 /Users/biocbuild/bbs-3.20-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 -- Mon Jun 10 12:59:59 2024 
*********************************************** 
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 
 19.716   0.984  20.773 

Example timings

bigmelon.Rcheck/bigmelon-Ex.timings

nameusersystemelapsed
GEOtoGDS0.0000.0010.001
app2gds0.4210.0360.486
backupGdsn0.2450.0280.283
bigmelon-accessors0.1770.0240.223
bigmelon-internal0.1050.0160.131
bigmelon-normalization4.5510.1734.742
combogds0.4380.0720.535
es2gds0.2580.0430.311
finalreport2gds000
gds2mlumi0.4150.0290.453
getquantilesandranks0.2950.0310.337
iadd35.458 1.60437.181
pfiltergds0.3840.0390.433
prcompgdsn0.2490.0280.286
pwodgdsn0.4200.0310.461
rankednorm0.2530.0270.289
redirect0.2560.0300.294