Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:42 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for hiAnnotator on tokay2


To the developers/maintainers of the hiAnnotator package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hiAnnotator.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 864/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.28.0  (landing page)
Nirav V Malani
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/hiAnnotator
git_branch: RELEASE_3_14
git_last_commit: ac0785b
git_last_commit_date: 2021-10-26 12:13:40 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hiAnnotator
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hiAnnotator_1.28.0.tar.gz
StartedAt: 2022-04-12 21:05:25 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 21:10:36 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 310.7 seconds
RetCode: 0
Status:   OK  
CheckDir: hiAnnotator.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hiAnnotator_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/hiAnnotator.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.28.0'
* 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 ... OK
* 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 '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 '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'
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'
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 featureName
  keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths
  seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels
  subjectHits
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/hiAnnotator.Rcheck/00check.log'
for details.



Installation output

hiAnnotator.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/hiAnnotator_1.28.0.tar.gz && rm -rf hiAnnotator.buildbin-libdir && mkdir hiAnnotator.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hiAnnotator.buildbin-libdir hiAnnotator_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL hiAnnotator_1.28.0.zip && rm hiAnnotator_1.28.0.tar.gz hiAnnotator_1.28.0.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
 49  798k   49  394k    0     0   530k      0  0:00:01 --:--:--  0:00:01  530k
100  798k  100  798k    0     0   551k      0  0:00:01  0:00:01 --:--:--  551k

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  
    getNearestFeature                       html  
    getRelevantCol                          html  
    getSitesInFeature                       html  
    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_1.28.0.zip
* DONE (hiAnnotator)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'hiAnnotator' successfully unpacked and MD5 sums checked

Tests output


Example timings

hiAnnotator.Rcheck/examples_i386/hiAnnotator-Ex.timings

nameusersystemelapsed
cleanColname000
doAnnotation0.880.030.90
get2NearestFeature1.930.132.05
getFeatureCounts0.540.220.76
getFeatureCountsBig0.600.000.59
getLowestDists0.090.000.10
getNearestFeature1.170.011.19
getRelevantCol0.020.000.01
getSitesInFeature0.670.000.67
getUCSCtable000
getWindowLabel000
makeChunks0.410.040.44
makeGRanges0.430.000.44
makeUCSCsession000
plotdisFeature1.430.032.73

hiAnnotator.Rcheck/examples_x64/hiAnnotator-Ex.timings

nameusersystemelapsed
cleanColname000
doAnnotation1.980.022.00
get2NearestFeature1.470.051.52
getFeatureCounts0.750.060.81
getFeatureCountsBig0.710.000.71
getLowestDists0.100.000.11
getNearestFeature2.020.012.03
getRelevantCol0.020.000.01
getSitesInFeature0.710.020.74
getUCSCtable000
getWindowLabel000
makeChunks0.410.010.42
makeGRanges0.360.000.36
makeUCSCsession000
plotdisFeature1.170.021.19