Armen R. Karapetyan
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/transcriptR |
| Branch: RELEASE_3_8 |
| Last Commit: 777abcd |
| Last Changed Date: 2019-01-04 13:52:51 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:09 -0400 (Sat, 13 Apr 2019).
| Package 1578/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| transcriptR 1.10.1 Armen R. Karapetyan
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: transcriptR |
| Version: 1.10.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings transcriptR_1.10.1.tar.gz |
| StartedAt: 2019-04-13 05:59:48 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 06:09:16 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 568.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: transcriptR.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings transcriptR_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/transcriptR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.10.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/ChipDataSet-class.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/ChipDataSet-class.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:26: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:29: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/annotateTranscripts-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/annotateTranscripts-methods.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/breakTranscriptsByPeaks-methods.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructCDS.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructCDS.Rd:22: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructCDS.Rd:44: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructCDS.Rd:65: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructTDS.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructTDS.Rd:29: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructTDS.Rd:49: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/detectTranscripts-methods.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/detectTranscripts-methods.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/estimateGapDistance-methods.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/getPeaks-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/getTranscripts-methods.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-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
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
breakTranscriptsByPeaks-methods 8.59 0.75 9.39
peaksToBed-methods 5.51 0.34 5.86
predictStrand-methods 5.20 0.28 5.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
breakTranscriptsByPeaks-methods 9.97 0.44 10.41
peaksToBed-methods 5.08 0.20 5.28
predictStrand-methods 4.96 0.20 5.18
* 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-3.8-bioc/meat/transcriptR.Rcheck/00check.log'
for details.
transcriptR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/transcriptR_1.10.1.tar.gz && rm -rf transcriptR.buildbin-libdir && mkdir transcriptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transcriptR.buildbin-libdir transcriptR_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL transcriptR_1.10.1.zip && rm transcriptR_1.10.1.tar.gz transcriptR_1.10.1.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 2472k 100 2472k 0 0 30.3M 0 --:--:-- --:--:-- --:--:-- 31.7M
install for i386
* installing *source* package 'transcriptR' ...
** R
** data
** inst
** byte-compile and prepare 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-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/ChipDataSet-class.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/ChipDataSet-class.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
TranscriptionDataSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:26: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:29: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/TranscriptionDataSet-class.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
addFeature-methods html
annot html
finding level-2 HTML links ... done
annotateTranscripts-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/annotateTranscripts-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/annotateTranscripts-methods.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
breakTranscriptsByPeaks-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/breakTranscriptsByPeaks-methods.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
cds html
constructCDS html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructCDS.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructCDS.Rd:22: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructCDS.Rd:44: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructCDS.Rd:65: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
constructTDS html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructTDS.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructTDS.Rd:29: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/constructTDS.Rd:49: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
detectTranscripts-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/detectTranscripts-methods.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/detectTranscripts-methods.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
estimateBackground-methods html
estimateGapDistance-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/estimateGapDistance-methods.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
exportCoverage-methods html
getConfusionMatrix-methods html
getGenomicAnnot-methods html
getPeaks-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/getPeaks-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
getPredictorSignificance-methods html
getProbTreshold-methods html
getQuadProb-methods html
getTestedGapDistances-methods html
getTranscripts-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYLxCWu/R.INSTALL26e45a4e4b8c/transcriptR/man/getTranscripts-methods.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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_1.10.1.zip
* DONE (transcriptR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'transcriptR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
transcriptR.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
55.45 3.20 59.79
|
transcriptR.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
55.62 1.67 57.29
|
|
transcriptR.Rcheck/examples_i386/transcriptR-Ex.timings
|
transcriptR.Rcheck/examples_x64/transcriptR-Ex.timings
|