Martin Morgan
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RaggedExperiment |
| Branch: master |
| Last Commit: 2ee0afb |
| Last Changed Date: 2019-03-22 14:30:28 -0400 (Fri, 22 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:30:43 -0400 (Tue, 09 Apr 2019).
| Package 1279/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RaggedExperiment 1.7.5 Martin Morgan
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: RaggedExperiment |
| Version: 1.7.5 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RaggedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RaggedExperiment_1.7.5.tar.gz |
| StartedAt: 2019-04-09 05:12:59 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:16:51 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 231.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RaggedExperiment.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RaggedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RaggedExperiment_1.7.5.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RaggedExperiment.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'RaggedExperiment/DESCRIPTION' ... OK * this is package 'RaggedExperiment' version '1.7.5' * 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 'RaggedExperiment' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:107: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:131: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:132: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:133: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:142: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:144: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:157: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:162: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:163: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:172: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:405: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:419: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RaggedExperiment.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 ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'S4Vectors:::selectSome' See the note in ?`:::` about the use of this operator. * 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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RaggedExperiment.Rcheck/00check.log' for details.
RaggedExperiment.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RaggedExperiment_1.7.5.tar.gz && rm -rf RaggedExperiment.buildbin-libdir && mkdir RaggedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RaggedExperiment.buildbin-libdir RaggedExperiment_1.7.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RaggedExperiment_1.7.5.zip && rm RaggedExperiment_1.7.5.tar.gz RaggedExperiment_1.7.5.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 24800 100 24800 0 0 398k 0 --:--:-- --:--:-- --:--:-- 448k
install for i386
* installing *source* package 'RaggedExperiment' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RaggedExperiment'
finding HTML links ... done
RaggedExperiment-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:107: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:131: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:132: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:133: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:142: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:144: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:157: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:162: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:163: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:172: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:405: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiQTWWH/R.INSTALL1f0837bd7c53/RaggedExperiment/man/RaggedExperiment-class.Rd:419: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
RaggedExperiment-package html
assay-functions html
coerce-functions 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 'RaggedExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RaggedExperiment' as RaggedExperiment_1.7.5.zip
* DONE (RaggedExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RaggedExperiment' successfully unpacked and MD5 sums checked
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RaggedExperiment.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(RaggedExperiment)
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, colMeans, colSums, 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, rowMeans, rowSums,
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("RaggedExperiment")
== testthat results ===========================================================
OK: 132 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
16.70 0.51 17.20
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RaggedExperiment.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(RaggedExperiment)
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, colMeans, colSums, 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, rowMeans, rowSums,
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("RaggedExperiment")
== testthat results ===========================================================
OK: 132 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
19.09 0.39 19.45
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RaggedExperiment.Rcheck/examples_i386/RaggedExperiment-Ex.timings
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RaggedExperiment.Rcheck/examples_x64/RaggedExperiment-Ex.timings
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