Nirav V Malani
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/hiAnnotator |
| Branch: RELEASE_3_8 |
| Last Commit: f7b67a6 |
| Last Changed Date: 2018-10-30 11:41:54 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:54 -0400 (Sat, 13 Apr 2019).
| Package 716/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hiAnnotator 1.16.0 Nirav V Malani
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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: hiAnnotator |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings hiAnnotator_1.16.0.tar.gz |
| StartedAt: 2019-04-13 03:00:46 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:05:51 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 304.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hiAnnotator.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings hiAnnotator_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/hiAnnotator.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 'hiAnnotator/DESCRIPTION' ... OK
* this is package 'hiAnnotator' version '1.16.0'
* 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 'hiAnnotator' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpW8bifW/R.INSTALL40c14991d92/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-3.8-bioc/tmpdir/RtmpW8bifW/R.INSTALL40c14991d92/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-3.8-bioc/tmpdir/RtmpW8bifW/R.INSTALL40c14991d92/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-3.8-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 : <anonymous>: no visible binding for global
variable 'queryHits'
get2NearestFeature : <anonymous>: no visible binding for global
variable 'dist'
get2NearestFeature : <anonymous>: no visible binding for global
variable 'featureName'
getFeatureCounts : <anonymous>: 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 : <anonymous>: no visible global function definition for
'keepSeqlevels'
makeChunks : <anonymous>: 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
** 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-3.8-bioc/meat/hiAnnotator.Rcheck/00check.log'
for details.
hiAnnotator.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/hiAnnotator_1.16.0.tar.gz && rm -rf hiAnnotator.buildbin-libdir && mkdir hiAnnotator.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hiAnnotator.buildbin-libdir hiAnnotator_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL hiAnnotator_1.16.0.zip && rm hiAnnotator_1.16.0.tar.gz hiAnnotator_1.16.0.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 795k 100 795k 0 0 16.8M 0 --:--:-- --:--:-- --:--:-- 18.4M
install for i386
* installing *source* package 'hiAnnotator' ...
** 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-3.8-bioc/tmpdir/RtmpW8bifW/R.INSTALL40c14991d92/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-3.8-bioc/tmpdir/RtmpW8bifW/R.INSTALL40c14991d92/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-3.8-bioc/tmpdir/RtmpW8bifW/R.INSTALL40c14991d92/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
In R CMD INSTALL
install for x64
* installing *source* package 'hiAnnotator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hiAnnotator' as hiAnnotator_1.16.0.zip
* DONE (hiAnnotator)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'hiAnnotator' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
hiAnnotator.Rcheck/examples_i386/hiAnnotator-Ex.timings
|
hiAnnotator.Rcheck/examples_x64/hiAnnotator-Ex.timings
|