Tyler J. Gorrie-Stone
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/bigmelon |
| git_branch: master |
| git_last_commit: 8a43e71 |
| git_last_commit_date: 2021-10-26 12:30:04 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:00 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the bigmelon package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 146/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bigmelon 1.21.0 (landing page) Tyler J. Gorrie-Stone
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: bigmelon |
| Version: 1.21.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bigmelon.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings bigmelon_1.21.0.tar.gz |
| StartedAt: 2022-03-17 18:31:35 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:37:10 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 335.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: bigmelon.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bigmelon.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings bigmelon_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/bigmelon.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.21.0'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
iadd 30.03 3.15 33.24
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/bigmelon.Rcheck/00check.log'
for details.
bigmelon.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL bigmelon
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
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
* DONE (bigmelon)
Making 'packages.html' ... done
bigmelon.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 D:\biocbuild\bbs-3.15-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 -- Thu Mar 17 18:36:54 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
13.25 1.48 14.73
bigmelon.Rcheck/bigmelon-Ex.timings
| name | user | system | elapsed | |
| GEOtoGDS | 0 | 0 | 0 | |
| app2gds | 0.29 | 0.06 | 0.36 | |
| backupGdsn | 0.18 | 0.02 | 0.19 | |
| bigmelon-accessors | 0.18 | 0.05 | 0.23 | |
| bigmelon-internal | 0.14 | 0.01 | 0.16 | |
| bigmelon-normalization | 2.14 | 0.14 | 2.31 | |
| combogds | 0.29 | 0.03 | 0.31 | |
| es2gds | 0.14 | 0.04 | 0.19 | |
| finalreport2gds | 0 | 0 | 0 | |
| gds2mlumi | 0.34 | 0.03 | 0.38 | |
| getquantilesandranks | 0.22 | 0.03 | 0.54 | |
| iadd | 30.03 | 3.15 | 33.24 | |
| pfiltergds | 0.20 | 0.05 | 0.25 | |
| prcompgdsn | 0.13 | 0.03 | 0.15 | |
| pwodgdsn | 0.26 | 0.02 | 0.28 | |
| rankednorm | 0.14 | 0.01 | 0.16 | |
| redirect | 0.13 | 0.03 | 0.16 | |