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CHECK report for hiAnnotator on tokay1

This page was generated on 2020-11-23 12:20:53 -0500 (Mon, 23 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE hiAnnotator PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 827/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.24.0
Nirav V Malani
Snapshot Date: 2020-11-22 14:42:09 -0500 (Sun, 22 Nov 2020)
URL: https://git.bioconductor.org/packages/hiAnnotator
Branch: RELEASE_3_12
Last Commit: ab43fdd
Last Changed Date: 2020-10-27 10:56:46 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hiAnnotator
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings hiAnnotator_1.24.0.tar.gz
StartedAt: 2020-11-23 03:54:48 -0500 (Mon, 23 Nov 2020)
EndedAt: 2020-11-23 04:00:42 -0500 (Mon, 23 Nov 2020)
EllapsedTime: 354.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: hiAnnotator.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings hiAnnotator_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/hiAnnotator.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.24.0'
* 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-3.12-bioc/tmpdir/RtmpI3e83g/R.INSTALL235436c67b4/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-3.12-bioc/tmpdir/RtmpI3e83g/R.INSTALL235436c67b4/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-3.12-bioc/tmpdir/RtmpI3e83g/R.INSTALL235436c67b4/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-3.12-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-3.12-bioc/meat/hiAnnotator.Rcheck/00check.log'
for details.



Installation output

hiAnnotator.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/hiAnnotator_1.24.0.tar.gz && rm -rf hiAnnotator.buildbin-libdir && mkdir hiAnnotator.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hiAnnotator.buildbin-libdir hiAnnotator_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL hiAnnotator_1.24.0.zip && rm hiAnnotator_1.24.0.tar.gz hiAnnotator_1.24.0.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
  0  795k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  795k  100  795k    0     0  3511k      0 --:--:-- --:--:-- --:--:-- 3567k

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  
    dot-checkArgsSetDefaults                html  
    dot-mergeAndReturn                      html  
    genes                                   html  
    get2NearestFeature                      html  
    getFeatureCounts                        html  
    getFeatureCountsBig                     html  
    getLowestDists                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI3e83g/R.INSTALL235436c67b4/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-3.12-bioc/tmpdir/RtmpI3e83g/R.INSTALL235436c67b4/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-3.12-bioc/tmpdir/RtmpI3e83g/R.INSTALL235436c67b4/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_1.24.0.zip
* DONE (hiAnnotator)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'hiAnnotator' successfully unpacked and MD5 sums checked

Tests output


Example timings

hiAnnotator.Rcheck/examples_i386/hiAnnotator-Ex.timings

nameusersystemelapsed
cleanColname000
doAnnotation1.470.341.82
get2NearestFeature2.750.463.21
getFeatureCounts0.980.151.14
getFeatureCountsBig1.070.041.09
getLowestDists0.120.000.12
getNearestFeature2.060.062.13
getRelevantCol0.000.010.01
getSitesInFeature0.990.051.03
getUCSCtable0.000.020.02
getWindowLabel000
makeChunks0.530.010.55
makeGRanges0.560.000.57
makeUCSCsession000
plotdisFeature2.040.022.06

hiAnnotator.Rcheck/examples_x64/hiAnnotator-Ex.timings

nameusersystemelapsed
cleanColname000
doAnnotation1.030.021.05
get2NearestFeature2.540.062.64
getFeatureCounts0.730.030.77
getFeatureCountsBig0.530.050.58
getLowestDists0.060.000.06
getNearestFeature1.220.011.23
getRelevantCol0.020.000.02
getSitesInFeature0.670.000.67
getUCSCtable000
getWindowLabel000
makeChunks0.370.020.39
makeGRanges0.330.020.34
makeUCSCsession000
plotdisFeature1.500.001.71