| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-11-22 11:34 -0500 (Fri, 22 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
| 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 1959/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SingleMoleculeFootprinting 2.1.0 (landing page) Guido Barzaghi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the SingleMoleculeFootprinting package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleMoleculeFootprinting.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. |
| Package: SingleMoleculeFootprinting |
| Version: 2.1.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SingleMoleculeFootprinting.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SingleMoleculeFootprinting_2.1.0.tar.gz |
| StartedAt: 2024-11-22 05:33:28 -0500 (Fri, 22 Nov 2024) |
| EndedAt: 2024-11-22 05:41:00 -0500 (Fri, 22 Nov 2024) |
| EllapsedTime: 452.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SingleMoleculeFootprinting.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SingleMoleculeFootprinting.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SingleMoleculeFootprinting_2.1.0.tar.gz
###
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##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SingleMoleculeFootprinting/DESCRIPTION' ... OK
* this is package 'SingleMoleculeFootprinting' version '2.1.0'
* 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 'SingleMoleculeFootprinting' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'Biostrings::setequal' by 'dplyr::setequal' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'GenomicRanges::intersect' by 'dplyr::intersect' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'Biostrings::collapse' by 'dplyr::collapse' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'BiocGenerics::boxplot' by 'graphics::boxplot' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'Matrix::image' by 'graphics::image' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'dplyr::between' by 'plyranges::between' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'dplyr::n_distinct' by 'plyranges::n_distinct' when loading 'SingleMoleculeFootprinting'
Warning: replacing previous import 'dplyr::n' by 'plyranges::n' when loading 'SingleMoleculeFootprinting'
See 'E:/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Create_MethylationCallingWindows: no visible binding for global
variable 'idx'
GRanges_to_DF: no visible binding for global variable 'Sample'
GRanges_to_DF: no visible binding for global variable 'Score'
LowCoverageMethRate_RMSE: no visible binding for global variable
'Sample'
PlotAvgSMF: no visible binding for global variable 'MethRate'
PlotSingleMoleculeStack : <anonymous>: no visible binding for global
variable 'Coordinate'
PlotSingleMoleculeStack : <anonymous>: no visible binding for global
variable 'Methylation'
PlotSingleMoleculeStack: no visible binding for global variable
'Sample'
StateQuantificationPlot: no visible binding for global variable 'State'
StateQuantificationPlot: no visible binding for global variable
'Pattern'
StateQuantificationPlot: no visible binding for global variable 'Bin'
StateQuantificationPlot: no visible binding for global variable
'Methylation'
Undefined global functions or variables:
Bin Coordinate MethRate Methylation Pattern Sample Score State idx
* 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 ... NOTE
S3 methods shown with full name in Rd file 'cbind.fill.Matrix.Rd':
'cbind.fill.Matrix'
S3 methods shown with full name in Rd file 'rbind.fill.Matrix.Rd':
'rbind.fill.Matrix'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GetSingleMolMethMat 13.73 0.57 14.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.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: 1 WARNING, 2 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log'
for details.
SingleMoleculeFootprinting.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SingleMoleculeFootprinting ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'SingleMoleculeFootprinting' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'Biostrings::setequal' by 'dplyr::setequal' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::intersect' by 'dplyr::intersect' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'Biostrings::collapse' by 'dplyr::collapse' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::boxplot' by 'graphics::boxplot' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'Matrix::image' by 'graphics::image' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::between' by 'plyranges::between' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::n_distinct' by 'plyranges::n_distinct' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::n' by 'plyranges::n' when loading 'SingleMoleculeFootprinting' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'Biostrings::setequal' by 'dplyr::setequal' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::intersect' by 'dplyr::intersect' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'Biostrings::collapse' by 'dplyr::collapse' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::boxplot' by 'graphics::boxplot' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'Matrix::image' by 'graphics::image' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::between' by 'plyranges::between' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::n_distinct' by 'plyranges::n_distinct' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::n' by 'plyranges::n' when loading 'SingleMoleculeFootprinting' ** testing if installed package can be loaded from final location Warning: replacing previous import 'Biostrings::setequal' by 'dplyr::setequal' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::intersect' by 'dplyr::intersect' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'Biostrings::collapse' by 'dplyr::collapse' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'BiocGenerics::boxplot' by 'graphics::boxplot' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'Matrix::image' by 'graphics::image' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::between' by 'plyranges::between' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::n_distinct' by 'plyranges::n_distinct' when loading 'SingleMoleculeFootprinting' Warning: replacing previous import 'dplyr::n' by 'plyranges::n' when loading 'SingleMoleculeFootprinting' ** testing if installed package keeps a record of temporary installation path * DONE (SingleMoleculeFootprinting)
SingleMoleculeFootprinting.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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(SingleMoleculeFootprinting)
There were 12 warnings (use warnings() to see them)
>
> test_check("SingleMoleculeFootprinting")
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
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: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: BiocIO
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:BiocIO':
FileForFormat
all necessary alignment files found
Detected experiment type: DE
all necessary alignment files found
see ?SingleMoleculeFootprintingData and browseVignettes('SingleMoleculeFootprintingData') for documentation
loading from cache
counting alignments...done
counting alignments...done
all necessary alignment files found
5334 reads found mapping to the - strand, collapsing to +
5334 reads found mapping to the - strand, collapsing to +
Detected experiment type: DE
Collecting summarized methylation for bins
Subsetting those reads that cover all bins
Summarizing reads into patterns
Splitting reads by pattern
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
>
> proc.time()
user system elapsed
47.14 3.82 51.26
SingleMoleculeFootprinting.Rcheck/SingleMoleculeFootprinting-Ex.timings
| name | user | system | elapsed | |
| Arrange_TFBSs_clusters | 0.50 | 0.01 | 0.71 | |
| BaitCapture | 0 | 0 | 0 | |
| BinMethylation | 0.22 | 0.03 | 0.25 | |
| CallContextMethylation | 0 | 0 | 0 | |
| CollapseStrands | 0 | 0 | 0 | |
| CollapseStrandsSM | 0 | 0 | 0 | |
| CollectCompositeData | 0 | 0 | 0 | |
| CompositeMethylationCorrelation | 0 | 0 | 0 | |
| CompositePlot | 0.00 | 0.02 | 0.01 | |
| ConversionRate | 0 | 0 | 0 | |
| Create_MethylationCallingWindows | 0.08 | 0.00 | 0.08 | |
| DetectExperimentType | 0.72 | 0.03 | 0.77 | |
| FilterByConversionRate | 0.67 | 0.16 | 0.89 | |
| FilterContextCytosines | 0.44 | 0.04 | 0.48 | |
| GetQuasRprj | 2.14 | 1.61 | 3.75 | |
| GetSingleMolMethMat | 13.73 | 0.57 | 14.36 | |
| MaskSNPs | 0.11 | 0.03 | 0.14 | |
| PlotAvgSMF | 0.55 | 0.03 | 0.58 | |
| PlotSM | 0.87 | 0.01 | 0.89 | |
| PlotSingleMoleculeStack | 1.14 | 0.09 | 1.23 | |
| PlotSingleSiteSMF | 2.10 | 0.16 | 2.25 | |
| SingleTFStates | 0 | 0 | 0 | |
| SortReads | 0.23 | 0.02 | 0.25 | |
| SortReadsBySingleTF | 0.06 | 0.00 | 0.07 | |
| SortReadsBySingleTF_MultiSiteWrapper | 0 | 0 | 0 | |
| SortReadsByTFCluster | 0.06 | 0.00 | 0.06 | |
| SortReadsByTFCluster_MultiSiteWrapper | 0 | 0 | 0 | |
| StateQuantification | 0.11 | 0.00 | 0.11 | |
| StateQuantificationBySingleTF | 0.05 | 0.00 | 0.05 | |
| StateQuantificationByTFPair | 0.05 | 0.01 | 0.06 | |
| StateQuantificationPlot | 0.50 | 0.02 | 0.51 | |
| TFPairStates | 0.01 | 0.00 | 0.02 | |
| cbind.fill.Matrix | 0.50 | 0.22 | 0.72 | |
| rbind.fill.Matrix | 0.56 | 0.26 | 0.83 | |