Armen R. Karapetyan
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/transcriptR |
| Branch: RELEASE_3_6 |
| Last Commit: 4487ae8 |
| Last Changed Date: 2017-10-30 12:41:10 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:14 -0400 (Thu, 12 Apr 2018).
| Package 1414/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| transcriptR 1.6.0 Armen R. Karapetyan
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: transcriptR |
| Version: 1.6.0 |
| Command: rm -rf transcriptR.buildbin-libdir transcriptR.Rcheck && mkdir transcriptR.buildbin-libdir transcriptR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.6.0.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.6.0.tar.gz |
| StartedAt: 2018-04-12 03:38:20 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:49:09 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 648.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: transcriptR.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf transcriptR.buildbin-libdir transcriptR.Rcheck && mkdir transcriptR.buildbin-libdir transcriptR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.6.0.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/transcriptR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'transcriptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'transcriptR' version '1.6.0'
* 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 'transcriptR' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/ChipDataSet-class.Rd:15: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/ChipDataSet-class.Rd:17: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:18: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:23: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:26: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:29: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:43: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/annotateTranscripts-methods.Rd:17: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/annotateTranscripts-methods.Rd:24: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/breakTranscriptsByPeaks-methods.Rd:25: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructCDS.Rd:18: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructCDS.Rd:22: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructCDS.Rd:44: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructCDS.Rd:65: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructTDS.Rd:13: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructTDS.Rd:29: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructTDS.Rd:49: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/detectTranscripts-methods.Rd:42: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/detectTranscripts-methods.Rd:47: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/estimateGapDistance-methods.Rd:20: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/getPeaks-methods.Rd:17: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/getTranscripts-methods.Rd:26: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/transcriptR.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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
breakTranscriptsByPeaks-methods 11.53 0.61 12.70
predictStrand-methods 7.00 0.25 7.31
peaksToBed-methods 6.92 0.19 7.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
breakTranscriptsByPeaks-methods 16.65 0.37 17.64
predictStrand-methods 8.31 0.41 8.72
peaksToBed-methods 7.89 0.14 8.03
plotFeatures-methods 5.53 0.00 5.57
* 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-3.6-bioc/meat/transcriptR.Rcheck/00check.log'
for details.
transcriptR.Rcheck/00install.out
install for i386
* installing *source* package 'transcriptR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'transcriptR'
finding HTML links ... done
ChipDataSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/ChipDataSet-class.Rd:15: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/ChipDataSet-class.Rd:17: missing file link 'GRanges'
TranscriptionDataSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:18: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:23: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:26: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:29: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/TranscriptionDataSet-class.Rd:43: missing file link 'GRanges'
addFeature-methods html
annot html
finding level-2 HTML links ... done
annotateTranscripts-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/annotateTranscripts-methods.Rd:17: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/annotateTranscripts-methods.Rd:24: missing file link 'GRanges'
breakTranscriptsByPeaks-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/breakTranscriptsByPeaks-methods.Rd:25: missing file link 'GRanges'
cds html
constructCDS html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructCDS.Rd:18: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructCDS.Rd:22: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructCDS.Rd:44: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructCDS.Rd:65: missing file link 'GRanges'
constructTDS html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructTDS.Rd:13: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructTDS.Rd:29: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/constructTDS.Rd:49: missing file link 'coverage'
detectTranscripts-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/detectTranscripts-methods.Rd:42: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/detectTranscripts-methods.Rd:47: missing file link 'GRanges'
estimateBackground-methods html
estimateGapDistance-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/estimateGapDistance-methods.Rd:20: missing file link 'GRanges'
exportCoverage-methods html
getConfusionMatrix-methods html
getGenomicAnnot-methods html
getPeaks-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/getPeaks-methods.Rd:17: missing file link 'GRanges'
getPredictorSignificance-methods html
getProbTreshold-methods html
getQuadProb-methods html
getTestedGapDistances-methods html
getTranscripts-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyOTRvT/R.INSTALL389473cf66f2/transcriptR/man/getTranscripts-methods.Rd:26: missing file link 'GRanges'
peaksToBed-methods html
plotErrorRate-methods html
plotFeatures-methods html
plotGenomicAnnot-methods html
plotROC-methods html
predictStrand-methods html
predictTssOverlap-methods html
show html
tds html
transcriptsToBed-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'transcriptR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transcriptR' as transcriptR_1.6.0.zip
* DONE (transcriptR)
In R CMD INSTALL
In R CMD INSTALL
|
transcriptR.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(transcriptR)
>
> test_check("transcriptR")
== testthat results ===========================================================
OK: 87 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
61.65 2.07 63.71
|
transcriptR.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(transcriptR)
>
> test_check("transcriptR")
== testthat results ===========================================================
OK: 87 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
82.84 1.42 85.14
|
|
transcriptR.Rcheck/examples_i386/transcriptR-Ex.timings
|
transcriptR.Rcheck/examples_x64/transcriptR-Ex.timings
|