Panagiotis Moulos
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/recoup |
| git_branch: RELEASE_3_13 |
| git_last_commit: ab6d090 |
| git_last_commit_date: 2021-10-06 15:09:30 -0400 (Wed, 06 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:18 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the recoup package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recoup.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 1544/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recoup 1.20.1 (landing page) Panagiotis Moulos
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: recoup |
| Version: 1.20.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:recoup.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings recoup_1.20.1.tar.gz |
| StartedAt: 2021-10-15 04:17:20 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:27:19 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 598.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: recoup.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:recoup.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings recoup_1.20.1.tar.gz
###
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##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/recoup.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'recoup/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'recoup' version '1.20.1'
* 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 'recoup' can be installed ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
'GenomicFeatures:::GFF_FEATURE_TYPES' 'biomaRt:::.generateFilterXML'
'biomaRt:::.setResultColNames' 'biomaRt:::martCheck'
'biomaRt:::martDataset' 'biomaRt:::martHost' 'biomaRt:::martVSchema'
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
readBamIntervals: no visible binding for global variable 'bam.file'
recoupCorrelation: no visible binding for global variable 'Index'
recoupCorrelation: no visible binding for global variable 'Coverage'
recoupCorrelation: no visible binding for global variable 'Condition'
recoupCorrelation: no visible binding for global variable 'Design'
recoupHeatmap : <anonymous>: no visible global function definition for
'grid.text'
recoupProfile: no visible binding for global variable 'Signal'
recoupProfile: no visible binding for global variable 'Condition'
recoupProfile: no visible binding for global variable 'Design'
Undefined global functions or variables:
Condition Coverage Design Index Signal bam.file grid.text
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mergeRuns 17.66 0.33 17.98
profileMatrix 9.83 0.08 9.91
getAnnotation 7.97 0.04 11.11
recoupPlot 7.55 0.03 7.57
recoup 7.04 0.25 7.29
sliceObj 6.44 0.00 6.44
simpleGetSet 6.39 0.00 6.40
kmeansDesign 6.17 0.15 6.33
recoupHeatmap 5.08 0.04 5.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mergeRuns 18.63 0.12 18.75
profileMatrix 10.95 0.14 11.10
recoup 7.77 0.07 7.82
kmeansDesign 7.65 0.05 7.70
recoupPlot 7.36 0.13 7.49
sliceObj 7.45 0.01 7.47
simpleGetSet 7.13 0.00 7.13
getAnnotation 5.70 0.04 8.85
recoupProfile 5.47 0.03 5.70
recoupHeatmap 5.09 0.08 5.17
recoupCorrelation 5.12 0.04 5.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/recoup.Rcheck/00check.log'
for details.
recoup.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/recoup_1.20.1.tar.gz && rm -rf recoup.buildbin-libdir && mkdir recoup.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=recoup.buildbin-libdir recoup_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL recoup_1.20.1.zip && rm recoup_1.20.1.tar.gz recoup_1.20.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2018k 100 2018k 0 0 2712k 0 --:--:-- --:--:-- --:--:-- 2717k
install for i386
* installing *source* package 'recoup' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'recoup'
finding HTML links ... done
buildAnnotationDatabase html
buildAnnotationStore html
buildCustomAnnotation html
calcCoverage html
coverageRef html
finding level-2 HTML links ... done
coverageRnaRef html
getAnnotation html
getBiotypes html
getInstalledAnnotations html
importCustomAnnotation html
kmeansDesign html
loadAnnotation html
mergeRuns html
preprocessRanges html
profileMatrix html
recoup-defunct html
recoup-deprecated html
recoup html
recoupCorrelation html
recoupHeatmap html
recoupPlot html
recoupProfile html
recoup_test_data html
removeData html
rpMatrix html
simpleGetSet html
sliceObj html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'recoup' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'recoup' as recoup_1.20.1.zip
* DONE (recoup)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'recoup' successfully unpacked and MD5 sums checked
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recoup.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("recoup")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
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
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
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'grid'
The following object is masked from 'package:Biostrings':
pattern
========================================
ComplexHeatmap version 2.8.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
The new InteractiveComplexHeatmap package can directly export static
complex heatmaps into an interactive Shiny app with zero effort. Have a try!
This message can be suppressed by:
suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
Getting main ranges for measurements
measurement type: chipseq
genomic region type: tss
Calculating requested regions coverage for WT H4K20me1
calculating total coverage
processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
calculating total coverage
processing chr12
Calculating profile for WT H4K20me1
Calculating profile for Set8KO H4K20me1
Constructing genomic coverage profile curve(s)
The resolution of the requested profiles will be lowered to avoid
increased computation time and/or storage space for heatmap profiles...
Calculating tss profile for WT H4K20me1
Calculating tss profile for Set8KO H4K20me1
Constructing genomic coverage heatmap(s)
Constructing coverage correlation profile curve(s)
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
Getting main ranges for measurements
measurement type: chipseq
genomic region type: genebody
Calculating requested regions coverage for WT H4K20me1
calculating total coverage
processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
calculating total coverage
processing chr12
Calculating profile for WT H4K20me1
center
upstream
downstream
Calculating profile for Set8KO H4K20me1
center
upstream
downstream
Constructing genomic coverage profile curve(s)
Using provided design to facet the coverage profiles
Constructing genomic coverage heatmap(s)
Using provided design to facet the coverage profiles
Constructing coverage correlation profile curve(s)
Using provided design to facet the coverage profiles
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
RUNIT TEST PROTOCOL -- Fri Oct 15 04:26:31 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
recoup RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
33.34 2.10 35.43
|
recoup.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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("recoup")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
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
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
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'grid'
The following object is masked from 'package:Biostrings':
pattern
========================================
ComplexHeatmap version 2.8.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
The new InteractiveComplexHeatmap package can directly export static
complex heatmaps into an interactive Shiny app with zero effort. Have a try!
This message can be suppressed by:
suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
Getting main ranges for measurements
measurement type: chipseq
genomic region type: tss
Calculating requested regions coverage for WT H4K20me1
calculating total coverage
processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
calculating total coverage
processing chr12
Calculating profile for WT H4K20me1
Calculating profile for Set8KO H4K20me1
Constructing genomic coverage profile curve(s)
The resolution of the requested profiles will be lowered to avoid
increased computation time and/or storage space for heatmap profiles...
Calculating tss profile for WT H4K20me1
Calculating tss profile for Set8KO H4K20me1
Constructing genomic coverage heatmap(s)
Constructing coverage correlation profile curve(s)
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
Getting main ranges for measurements
measurement type: chipseq
genomic region type: genebody
Calculating requested regions coverage for WT H4K20me1
calculating total coverage
processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
calculating total coverage
processing chr12
Calculating profile for WT H4K20me1
center
upstream
downstream
Calculating profile for Set8KO H4K20me1
center
upstream
downstream
Constructing genomic coverage profile curve(s)
Using provided design to facet the coverage profiles
Constructing genomic coverage heatmap(s)
Using provided design to facet the coverage profiles
Constructing coverage correlation profile curve(s)
Using provided design to facet the coverage profiles
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
RUNIT TEST PROTOCOL -- Fri Oct 15 04:27:10 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
recoup RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
37.34 0.87 38.40
|
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recoup.Rcheck/examples_i386/recoup-Ex.timings
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recoup.Rcheck/examples_x64/recoup-Ex.timings
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