Liz Ing-Simmons
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/GenomicInteractions |
| Branch: RELEASE_3_12 |
| Last Commit: 014f226 |
| Last Changed Date: 2020-10-27 10:59:15 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:28 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the GenomicInteractions package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 718/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicInteractions 1.24.0 (landing page) Liz Ing-Simmons
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GenomicInteractions |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicInteractions.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenomicInteractions_1.24.0.tar.gz |
| StartedAt: 2021-05-06 03:06:10 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:15:59 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 588.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicInteractions.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicInteractions.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenomicInteractions_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicInteractions.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicInteractions/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicInteractions' version '1.24.0'
* 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 'GenomicInteractions' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpauB5AR/R.INSTALL273c7bb24016/GenomicInteractions/man/getters.Rd:43: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpauB5AR/R.INSTALL273c7bb24016/GenomicInteractions/man/setters.Rd:27: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicInteractions.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
extdata 7.9Mb
* 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicInteractions.Rcheck/00check.log'
for details.
GenomicInteractions.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicInteractions_1.24.0.tar.gz && rm -rf GenomicInteractions.buildbin-libdir && mkdir GenomicInteractions.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicInteractions.buildbin-libdir GenomicInteractions_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicInteractions_1.24.0.zip && rm GenomicInteractions_1.24.0.tar.gz GenomicInteractions_1.24.0.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 3316k 100 3316k 0 0 50.7M 0 --:--:-- --:--:-- --:--:-- 51.4M
install for i386
* installing *source* package 'GenomicInteractions' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicInteractions'
finding HTML links ... done
GInteractions-subsetByFeatures-methods
html
GenomicInteractions-class html
GenomicInteractions-package html
GenomicInteractions html
InteractionHelpers html
InteractionTrack-class html
InteractionTrack html
annotateInteractions html
annotateRegions html
asBED-GInteractions-method html
availableDisplayPars html
calculateDistances html
categoriseInteractions html
countsBetweenAnchors-methods html
dot-importHicLib html
dot-importHomer html
dot-processChiapetName html
dot-readBam html
dot-readTwoBams html
dot-validateInput html
export.bed12 html
export.bedpe html
export.chiasig html
export.igraph html
get_binom_ligation_threshold html
get_self_ligation_threshold html
getters html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpauB5AR/R.INSTALL273c7bb24016/GenomicInteractions/man/getters.Rd:43: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
hg19.refseq.transcripts html
hic_example_data html
makeGenomicInteractionsFromFile html
mm9_refseq_promoters html
plotAvgViewpoint html
plotCisTrans html
plotCounts html
plotDists html
plotInteractionAnnotations html
plotSummaryStats html
plotViewpoint html
removeDups html
resetAnnotations html
sameStrand html
setters html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpauB5AR/R.INSTALL273c7bb24016/GenomicInteractions/man/setters.Rd:27: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
sum-GInteractions-method html
summariseByFeaturePairs html
summariseByFeatures html
thymus_enh html
updateObject-GenomicInteractions-method
html
viewPoint 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 'GenomicInteractions' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicInteractions' as GenomicInteractions_1.24.0.zip
* DONE (GenomicInteractions)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GenomicInteractions' successfully unpacked and MD5 sums checked
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GenomicInteractions.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.
> library(testthat)
> library(GenomicInteractions)
Loading required package: InteractionSet
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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
>
> test_check("GenomicInteractions")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 51 ]
>
> proc.time()
user system elapsed
21.31 1.87 25.09
|
GenomicInteractions.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(GenomicInteractions)
Loading required package: InteractionSet
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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
>
> test_check("GenomicInteractions")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 51 ]
>
> proc.time()
user system elapsed
22.03 0.76 24.36
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GenomicInteractions.Rcheck/examples_i386/GenomicInteractions-Ex.timings
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GenomicInteractions.Rcheck/examples_x64/GenomicInteractions-Ex.timings
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