Jialin Ma
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TnT |
| Branch: RELEASE_3_11 |
| Last Commit: 2818722 |
| Last Changed Date: 2020-04-27 15:11:27 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:56 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE TnT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1810/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TnT 1.10.0 Jialin Ma
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: TnT |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TnT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TnT_1.10.0.tar.gz |
| StartedAt: 2020-10-17 08:53:41 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:56:18 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 157.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TnT.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TnT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TnT_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TnT.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'TnT/DESCRIPTION' ... OK * this is package 'TnT' version '1.10.0' * 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 'TnT' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpU5D37e/R.INSTALL15e854f226dc/TnT/man/mapcol.Rd:13: file link 'terrain.colors' in package 'grDevices' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpU5D37e/R.INSTALL15e854f226dc/TnT/man/range-TnTBoard-method.Rd:12: file link 'range,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpU5D37e/R.INSTALL15e854f226dc/TnT/man/range-TnTTrack.Rd:16: file link 'range,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TnT.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 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 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 See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TnT.Rcheck/00check.log' for details.
TnT.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TnT_1.10.0.tar.gz && rm -rf TnT.buildbin-libdir && mkdir TnT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TnT.buildbin-libdir TnT_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TnT_1.10.0.zip && rm TnT_1.10.0.tar.gz TnT_1.10.0.zip
###
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install for i386
* installing *source* package 'TnT' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TnT'
finding HTML links ... done
TnT-shiny html
composite-track html
knit_print.TnTBoard html
mapcol html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpU5D37e/R.INSTALL15e854f226dc/TnT/man/mapcol.Rd:13: file link 'terrain.colors' in package 'grDevices' does not exist and so has been treated as a topic
range-TnTBoard-method html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpU5D37e/R.INSTALL15e854f226dc/TnT/man/range-TnTBoard-method.Rd:12: file link 'range,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
range-TnTTrack html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpU5D37e/R.INSTALL15e854f226dc/TnT/man/range-TnTTrack.Rd:16: file link 'range,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
saveTnT html
seqinfo html
strandlabel html
tntboard html
tooltip html
track-constructors html
trackSpec html
trackWidget html
trackdata html
tracklist 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 'TnT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TnT' as TnT_1.10.0.zip
* DONE (TnT)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TnT' successfully unpacked and MD5 sums checked
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TnT.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(TnT)
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, 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
>
> test_check("TnT")
== testthat results ===========================================================
[ OK: 36 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
5.59 0.39 5.96
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TnT.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(TnT)
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, 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
>
> test_check("TnT")
== testthat results ===========================================================
[ OK: 36 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
5.78 0.15 5.93
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TnT.Rcheck/examples_i386/TnT-Ex.timings
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TnT.Rcheck/examples_x64/TnT-Ex.timings
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