Armen R. Karapetyan
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/transcriptR |
| Branch: RELEASE_3_12 |
| Last Commit: 96add55 |
| Last Changed Date: 2020-10-27 11:10:00 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:01 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the transcriptR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1887/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| transcriptR 1.18.0 (landing page) Armen R. Karapetyan
| 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: transcriptR |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings transcriptR_1.18.0.tar.gz |
| StartedAt: 2021-05-06 07:39:33 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:51:48 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 735.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: transcriptR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings transcriptR_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/transcriptR.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 'transcriptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'transcriptR' version '1.18.0'
* 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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-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 (user + system) or elapsed time > 5s
user system elapsed
breakTranscriptsByPeaks-methods 11.18 0.59 11.79
predictStrand-methods 7.50 0.25 7.75
peaksToBed-methods 6.26 0.11 6.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
breakTranscriptsByPeaks-methods 12.61 0.25 12.86
predictStrand-methods 6.84 0.28 7.12
peaksToBed-methods 6.13 0.13 6.25
* 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-3.12-bioc/meat/transcriptR.Rcheck/00check.log'
for details.
transcriptR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/transcriptR_1.18.0.tar.gz && rm -rf transcriptR.buildbin-libdir && mkdir transcriptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transcriptR.buildbin-libdir transcriptR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL transcriptR_1.18.0.zip && rm transcriptR_1.18.0.tar.gz transcriptR_1.18.0.zip
###
##############################################################################
##############################################################################
% 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 18.5M 0 --:--:-- --:--:-- --:--:-- 18.7M
install for i386
* installing *source* package 'transcriptR' ...
** using staged installation
** 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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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-3.12-bioc/tmpdir/RtmpsJbXFa/R.INSTALL27b8db944ca/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 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 'transcriptR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transcriptR' as transcriptR_1.18.0.zip
* DONE (transcriptR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'transcriptR' successfully unpacked and MD5 sums checked
|
transcriptR.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(transcriptR)
>
> test_check("transcriptR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 87 ]
>
> proc.time()
user system elapsed
66.62 2.93 71.04
|
transcriptR.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(transcriptR)
>
> test_check("transcriptR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 87 ]
>
> proc.time()
user system elapsed
69.20 1.90 72.62
|
|
transcriptR.Rcheck/examples_i386/transcriptR-Ex.timings
|
transcriptR.Rcheck/examples_x64/transcriptR-Ex.timings
|