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CHECK report for intansv on tokay1

This page was generated on 2020-04-15 12:21:54 -0400 (Wed, 15 Apr 2020).

Package 850/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
intansv 1.26.1
Wen Yao
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/intansv
Branch: RELEASE_3_10
Last Commit: 8c93ffe
Last Changed Date: 2020-04-14 12:06:55 -0400 (Tue, 14 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK YES, new version is higher than in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: intansv
Version: 1.26.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:intansv.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings intansv_1.26.1.tar.gz
StartedAt: 2020-04-15 04:03:44 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:12:31 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 526.4 seconds
RetCode: 0
Status:  OK  
CheckDir: intansv.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:intansv.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings intansv_1.26.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/intansv.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'intansv/DESCRIPTION' ... OK
* this is package 'intansv' version '1.26.1'
* 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 'intansv' 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
DellyCluster: no visible global function definition for 'subjectHits'
LumpyCluster: no visible global function definition for 'subjectHits'
PindelCluster: no visible global function definition for 'subjectHits'
breakDancerCluster: no visible global function definition for
  'subjectHits'
mergeOLCNVs: no visible global function definition for 'subjectHits'
methodsMerge: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for 'queryHits'
plotChromosome: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for
  'seqlengths<-'
plotChromosome: no visible global function definition for 'seqlengths'
plotChromosome: no visible global function definition for 'aes'
plotRegion: no visible global function definition for 'seqlengths<-'
plotRegion: no visible global function definition for 'subjectHits'
plotRegion: no visible global function definition for 'aes'
plotRegion: no visible binding for global variable 'name'
readCnvnator: no visible global function definition for 'subjectHits'
readDelly: no visible global function definition for 'subjectHits'
readLumpy: no visible global function definition for 'subjectHits'
readPindel: no visible global function definition for 'subjectHits'
readSoftSearch: no visible global function definition for 'subjectHits'
readSvseq: no visible global function definition for 'subjectHits'
readSvseq : <anonymous>: no visible global function definition for
  'subjectHits'
softSearchCluster: no visible global function definition for
  'subjectHits'
tellOLPercantage: no visible global function definition for 'queryHits'
tellOLPercantage: no visible global function definition for
  'subjectHits'
Undefined global functions or variables:
  aes name queryHits seqlengths seqlengths<- 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
methodsMerge   33.41   1.86   36.55
readLumpy       6.28   0.00    6.53
plotChromosome  6.14   0.04    6.22
plotRegion      4.98   0.04    5.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
methodsMerge 23.46   0.25   23.72
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/intansv.Rcheck/00check.log'
for details.



Installation output

intansv.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/intansv_1.26.1.tar.gz && rm -rf intansv.buildbin-libdir && mkdir intansv.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=intansv.buildbin-libdir intansv_1.26.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL intansv_1.26.1.zip && rm intansv_1.26.1.tar.gz intansv_1.26.1.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
100  485k  100  485k    0     0  11.3M      0 --:--:-- --:--:-- --:--:-- 12.4M

install for i386

* installing *source* package 'intansv' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'intansv'
    finding HTML links ... done
    methodsMerge                            html  
    plotChromosome                          html  
    plotRegion                              html  
    readBreakDancer                         html  
    readCnvnator                            html  
    readDelly                               html  
    readLumpy                               html  
    readPindel                              html  
    readSoftSearch                          html  
    readSvseq                               html  
    svAnnotation                            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 'intansv' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'intansv' as intansv_1.26.1.zip
* DONE (intansv)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'intansv' successfully unpacked and MD5 sums checked

Tests output


Example timings

intansv.Rcheck/examples_i386/intansv-Ex.timings

nameusersystemelapsed
methodsMerge33.41 1.8636.55
plotChromosome6.140.046.22
plotRegion4.980.045.05
readBreakDancer1.080.001.08
readCnvnator0.690.000.68
readDelly3.260.003.27
readLumpy6.280.006.53
readPindel4.440.014.45
readSoftSearch0.440.000.48
readSvseq0.470.000.47
svAnnotation2.110.002.11

intansv.Rcheck/examples_x64/intansv-Ex.timings

nameusersystemelapsed
methodsMerge23.46 0.2523.72
plotChromosome4.450.034.48
plotRegion4.390.024.41
readBreakDancer1.060.001.06
readCnvnator0.660.000.66
readDelly2.640.002.64
readLumpy3.050.003.05
readPindel2.640.002.64
readSoftSearch0.290.000.29
readSvseq0.270.000.27
svAnnotation1.360.001.36