Nirav V Malani
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/hiAnnotator |
| Branch: RELEASE_3_9 |
| Last Commit: 537a9fe |
| Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:30:04 -0400 (Wed, 16 Oct 2019).
| Package 751/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hiAnnotator 1.18.0 Nirav V Malani
| 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 | |
| Package: hiAnnotator |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hiAnnotator_1.18.0.tar.gz |
| StartedAt: 2019-10-16 04:23:13 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:28:31 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 317.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hiAnnotator.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hiAnnotator_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/hiAnnotator.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'hiAnnotator/DESCRIPTION' ... OK * this is package 'hiAnnotator' 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 'hiAnnotator' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIZL6MA/R.INSTALL1ee016e66a3b/hiAnnotator/man/getLowestDists.Rd:32: file link 'nearest' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIZL6MA/R.INSTALL1ee016e66a3b/hiAnnotator/man/getLowestDists.Rd:19: file link 'nearest' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIZL6MA/R.INSTALL1ee016e66a3b/hiAnnotator/man/getSitesInFeature.Rd:38: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/hiAnnotator.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 ... NOTE get2NearestFeature: no visible global function definition for 'IRanges' get2NearestFeature: no visible global function definition for 'mid' get2NearestFeature: no visible binding for global variable 'dist' get2NearestFeature: no visible binding for global variable 'qStrand' get2NearestFeature: no visible binding for global variable 'subjectHits' get2NearestFeature :: no visible binding for global variable 'queryHits' get2NearestFeature : : no visible binding for global variable 'dist' get2NearestFeature : : no visible binding for global variable 'featureName' getFeatureCounts : : no visible global function definition for 'countQueryHits' getFeatureCountsBig: no visible global function definition for 'mid' getLowestDists: no visible binding for global variable 'queryHits' getLowestDists: no visible binding for global variable 'dist' getNearestFeature: no visible global function definition for 'IRanges' getNearestFeature: no visible global function definition for 'mid' getNearestFeature: no visible binding for global variable 'queryHits' getNearestFeature: no visible binding for global variable 'n' getNearestFeature: no visible binding for global variable 'featureName' getNearestFeature: no visible binding for global variable 'dist' getSitesInFeature: no visible global function definition for 'overlapsAny' getSitesInFeature: no visible binding for global variable 'queryHits' getSitesInFeature: no visible global function definition for 'n' getSitesInFeature: no visible binding for global variable 'featureName' makeChunks: no visible global function definition for 'breakInChunks' makeChunks: no visible global function definition for 'detectCores' makeChunks : : no visible global function definition for 'keepSeqlevels' makeChunks : : no visible global function definition for 'seqlevelsInUse' makeGRanges: no visible global function definition for 'IRanges' makeGRanges: no visible global function definition for 'seqlengths' makeGRanges: no visible global function definition for 'seqlevels<-' makeGRanges: no visible global function definition for 'sortSeqlevels' makeGRanges: no visible global function definition for 'seqlevelsInUse' makeGRanges: no visible global function definition for 'seqlengths<-' makeGRanges: no visible global function definition for 'seqlevels' Undefined global functions or variables: IRanges breakInChunks countQueryHits detectCores dist featureName keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels subjectHits Consider adding importFrom("stats", "dist") to your NAMESPACE file. * 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' ... NOTE The following directory looks like a leftover from 'knitr': 'figure' Please remove from your package. * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed getFeatureCounts 0.54 0.08 8.69 ** running examples for arch 'x64' ... 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/hiAnnotator.Rcheck/00check.log' for details.
hiAnnotator.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/hiAnnotator_1.18.0.tar.gz && rm -rf hiAnnotator.buildbin-libdir && mkdir hiAnnotator.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hiAnnotator.buildbin-libdir hiAnnotator_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL hiAnnotator_1.18.0.zip && rm hiAnnotator_1.18.0.tar.gz hiAnnotator_1.18.0.zip
###
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install for i386
* installing *source* package 'hiAnnotator' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'hiAnnotator'
finding HTML links ... done
cleanColname html
doAnnotation html
genes html
get2NearestFeature html
getFeatureCounts html
getFeatureCountsBig html
getLowestDists html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIZL6MA/R.INSTALL1ee016e66a3b/hiAnnotator/man/getLowestDists.Rd:32: file link 'nearest' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIZL6MA/R.INSTALL1ee016e66a3b/hiAnnotator/man/getLowestDists.Rd:19: file link 'nearest' in package 'IRanges' does not exist and so has been treated as a topic
getNearestFeature html
getRelevantCol html
getSitesInFeature html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIZL6MA/R.INSTALL1ee016e66a3b/hiAnnotator/man/getSitesInFeature.Rd:38: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
getUCSCtable html
finding level-2 HTML links ... done
getWindowLabel html
hiAnnotator html
makeChunks html
makeGRanges html
makeUCSCsession html
plotdisFeature html
sites html
sites.ctrl 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 'hiAnnotator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hiAnnotator' as hiAnnotator_1.18.0.zip
* DONE (hiAnnotator)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'hiAnnotator' successfully unpacked and MD5 sums checked
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hiAnnotator.Rcheck/examples_i386/hiAnnotator-Ex.timings
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hiAnnotator.Rcheck/examples_x64/hiAnnotator-Ex.timings
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