"Jacob Morrison"
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/biscuiteer |
| git_branch: master |
| git_last_commit: a17221f |
| git_last_commit_date: 2021-11-20 23:10:29 -0400 (Sat, 20 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:03 -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 biscuiteer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biscuiteer.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 196/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biscuiteer 1.9.2 (landing page) "Jacob Morrison"
| 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 | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: biscuiteer |
| Version: 1.9.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biscuiteer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biscuiteer_1.9.2.tar.gz |
| StartedAt: 2022-03-17 18:34:58 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:42:41 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 463.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biscuiteer.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biscuiteer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biscuiteer_1.9.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/biscuiteer.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 'biscuiteer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biscuiteer' version '1.9.2'
* package encoding: UTF-8
* 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 'biscuiteer' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer'
See 'D:/biocbuild/bbs-3.15-bioc/meat/biscuiteer.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 3.4Mb
* checking package directory ... 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'QDNAseq:::expectedVariance'
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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CpGindex 12.53 1.61 15.80
WGBSage 7.19 0.41 8.92
unionize 6.01 0.53 7.96
filterLoci 5.06 0.41 6.89
byExtremality 4.95 0.48 6.78
RRBSeq 4.90 0.31 5.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.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: 1 WARNING, 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/biscuiteer.Rcheck/00check.log'
for details.
biscuiteer.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL biscuiteer
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'biscuiteer' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer'
** help
*** installing help indices
converting help for package 'biscuiteer'
finding HTML links ... done
CpGindex html
ENSR_subset.hg19 html
ENSR_subset.hg38 html
GRCh37.chromArm html
GRCh38.chromArm html
H9state23unmeth.hg19 html
H9state23unmeth.hg38 html
HMM_CpG_islands.hg19 html
HMM_CpG_islands.hg38 html
RRBSeq html
WGBSage html
WGBSeq html
atRegions html
binCoverage html
biscuitMetadata html
biscuiteer-methods html
biscuiteer-package html
byChromArm html
byExtremality html
checkBiscuitBED html
clocks html
condenseSampleNames html
extremality html
fexpit html
filterLoci html
fixAge html
fixNAs html
flogit html
getClock html
getLogitFracMeth html
grToSeg html
hg19.chromArm html
hg38.chromArm html
makeBSseq html
readBiscuit html
segToGr html
seqinfo.hg19 html
seqinfo.hg38 html
seqinfo.mm10 html
simplifySampleNames html
summarizeBsSeqOver html
unionize html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer'
** testing if installed package keeps a record of temporary installation path
* DONE (biscuiteer)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'ChAMP' is missing or broken
done
biscuiteer.Rcheck/tests/testthat.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.
> library(testthat)
> library(biscuiteer)
Loading required package: biscuiteerData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
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
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading biscuiteerData.
Loading required package: bsseq
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
The following object is masked from 'package:ExperimentHub':
cache
The following object is masked from 'package:AnnotationHub':
cache
Warning message:
replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer'
>
> test_check("biscuiteer")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
20.04 1.89 23.67
biscuiteer.Rcheck/biscuiteer-Ex.timings
| name | user | system | elapsed | |
| CpGindex | 12.53 | 1.61 | 15.80 | |
| RRBSeq | 4.90 | 0.31 | 5.22 | |
| WGBSage | 7.19 | 0.41 | 8.92 | |
| WGBSeq | 3.42 | 0.22 | 3.64 | |
| atRegions | 3.26 | 0.18 | 4.16 | |
| binCoverage | 3.13 | 0.25 | 4.36 | |
| biscuitMetadata | 2.94 | 0.19 | 3.83 | |
| biscuiteer-package | 2.93 | 0.16 | 3.78 | |
| byChromArm | 1.94 | 0.20 | 2.94 | |
| byExtremality | 4.95 | 0.48 | 6.78 | |
| checkBiscuitBED | 0.13 | 0.00 | 0.12 | |
| condenseSampleNames | 0.05 | 0.02 | 0.06 | |
| extremality | 0 | 0 | 0 | |
| fexpit | 0 | 0 | 0 | |
| filterLoci | 5.06 | 0.41 | 6.89 | |
| fixAge | 0.03 | 0.00 | 0.03 | |
| fixNAs | 0 | 0 | 0 | |
| flogit | 0 | 0 | 0 | |
| getClock | 0.03 | 0.00 | 0.04 | |
| getLogitFracMeth | 3.36 | 0.16 | 4.20 | |
| grToSeg | 0.05 | 0.00 | 0.05 | |
| makeBSseq | 3.59 | 0.15 | 4.50 | |
| readBiscuit | 2.13 | 0.11 | 2.98 | |
| segToGr | 0.09 | 0.00 | 0.09 | |
| simplifySampleNames | 2.03 | 0.05 | 2.77 | |
| summarizeBsSeqOver | 2.35 | 0.17 | 3.20 | |
| unionize | 6.01 | 0.53 | 7.96 | |