Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:30 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 igvR on tokay2


To the developers/maintainers of the igvR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/igvR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 917/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.14.0  (landing page)
Paul Shannon
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/igvR
git_branch: RELEASE_3_14
git_last_commit: 2d7b52a
git_last_commit_date: 2021-10-26 12:44:17 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: igvR
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:igvR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings igvR_1.14.0.tar.gz
StartedAt: 2022-01-20 21:32:26 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 21:39:37 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 430.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: igvR.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:igvR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings igvR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/igvR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'igvR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'igvR' version '1.14.0'
* package encoding: UTF-8
* 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 'igvR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.6Mb
  sub-directories of 1Mb or more:
    browserCode   8.8Mb
    extdata       2.0Mb
* 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 ... WARNING
---- unloading
Error in .mergeMethodsTable(generic, mtable, tt, attach) : 
  trying to get slot "defined" from an object of a basic class ("environment") with no slots
Calls: unloadNamespace ... <Anonymous> -> .updateMethodsInTable -> .mergeMethodsTable
Execution halted
* 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 ... WARNING
---- unloading
Error in .mergeMethodsTable(generic, mtable, tt, attach) : 
  trying to get slot "defined" from an object of a basic class ("environment") with no slots
Calls: unloadNamespace ... <Anonymous> -> .updateMethodsInTable -> .mergeMethodsTable
Execution halted
* 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 ... 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 include directives in Makefiles ... 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 vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
  Found 'inst/doc/makefile': should be 'Makefile' and will be ignored
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/igvR.Rcheck/00check.log'
for details.



Installation output

igvR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/igvR_1.14.0.tar.gz && rm -rf igvR.buildbin-libdir && mkdir igvR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=igvR.buildbin-libdir igvR_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL igvR_1.14.0.zip && rm igvR_1.14.0.tar.gz igvR_1.14.0.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
 32 10.4M   32 3465k    0     0  3635k      0  0:00:02 --:--:--  0:00:02 3636k
 83 10.4M   83 8926k    0     0  4605k      0  0:00:02  0:00:01  0:00:01 4606k
100 10.4M  100 10.4M    0     0  4838k      0  0:00:02  0:00:02 --:--:-- 4840k

install for i386

* installing *source* package 'igvR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
  converting help for package 'igvR'
    finding HTML links ... done
    BedpeInteractionsTrack-class            html  
    DataFrameAnnotationTrack-class          html  
    DataFrameQuantitativeTrack-class        html  
    GRangesAnnotationTrack-class            html  
    GRangesQuantitativeTrack-class          html  
    GenomicAlignmentTrack-class             html  
    QuantitativeTrack-class                 html  
    RemoteAlignmentTrack-class              html  
    Track-class                             html  
    UCSCBedAnnotationTrack-class            html  
    UCSCBedGraphQuantitativeTrack-class     html  
    VariantTrack-class                      html  
    displayTrack                            html  
    enableMotifLogoPopups                   html  
    getGenomicRegion                        html  
    getSupportedGenomes                     html  
    getTrackNames                           html  
    igvAnnotationTrack-class                html  
    igvR-class                              html  
    ping                                    html  
    removeTracksByName                      html  
    saveToSVG                               html  
    setCustomGenome                         html  
    setGenome                               html  
    setTrackClickFunction                   html  
    showGenomicRegion                       html  
    showTrackLabels                         html  
    trackInfo                               html  
    trackSize-BedpeInteractionsTrack-method
                                            html  
    trackSize-DataFrameAnnotationTrack-method
                                            html  
    trackSize-DataFrameQuantitativeTrack-method
                                            html  
    trackSize-GRangesAnnotationTrack-method
                                            html  
    trackSize-GRangesQuantitativeTrack-method
                                            html  
    trackSize-GenomicAlignmentTrack-method
                                            html  
    trackSize-UCSCBedAnnotationTrack-method
                                            html  
    trackSize-UCSCBedGraphQuantitativeTrack-method
                                            html  
    trackSize-VariantTrack-method           html  
    trackSize                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'igvR' ...
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
* MD5 sums
packaged installation of 'igvR' as igvR_1.14.0.zip
* DONE (igvR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'igvR' successfully unpacked and MD5 sums checked

Tests output


Example timings

igvR.Rcheck/examples_i386/igvR-Ex.timings

nameusersystemelapsed
BedpeInteractionsTrack-class000
DataFrameAnnotationTrack-class0.020.000.02
DataFrameQuantitativeTrack-class0.020.000.01
GRangesAnnotationTrack-class0.040.000.05
GRangesQuantitativeTrack-class0.050.000.05
GenomicAlignmentTrack-class0.230.001.97
UCSCBedAnnotationTrack-class0.520.000.51
UCSCBedGraphQuantitativeTrack-class0.120.000.13
VariantTrack-class0.570.010.57
displayTrack000
enableMotifLogoPopups000
getGenomicRegion000
getSupportedGenomes000
getTrackNames000
igvR-class000
ping000
removeTracksByName000
setCustomGenome000
setGenome000
showGenomicRegion000
trackInfo000
trackSize-DataFrameAnnotationTrack-method0.010.000.02
trackSize-UCSCBedAnnotationTrack-method0.130.000.12

igvR.Rcheck/examples_x64/igvR-Ex.timings

nameusersystemelapsed
BedpeInteractionsTrack-class0.010.000.02
DataFrameAnnotationTrack-class0.020.000.01
DataFrameQuantitativeTrack-class0.020.000.02
GRangesAnnotationTrack-class0.060.000.06
GRangesQuantitativeTrack-class0.030.000.03
GenomicAlignmentTrack-class0.160.000.16
UCSCBedAnnotationTrack-class0.430.000.44
UCSCBedGraphQuantitativeTrack-class0.110.000.10
VariantTrack-class0.530.000.54
displayTrack000
enableMotifLogoPopups000
getGenomicRegion000
getSupportedGenomes000
getTrackNames000
igvR-class000
ping000
removeTracksByName000
setCustomGenome0.020.000.01
setGenome000
showGenomicRegion000
trackInfo000
trackSize-DataFrameAnnotationTrack-method000
trackSize-UCSCBedAnnotationTrack-method0.140.020.16