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CHECK report for IVAS on tokay1

This page was generated on 2018-04-12 13:25:40 -0400 (Thu, 12 Apr 2018).

Package 724/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 1.98.0
Seonggyun Han
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/IVAS
Branch: RELEASE_3_6
Last Commit: 91f8348
Last Changed Date: 2017-10-30 12:40:48 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IVAS
Version: 1.98.0
Command: rm -rf IVAS.buildbin-libdir IVAS.Rcheck && mkdir IVAS.buildbin-libdir IVAS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IVAS.buildbin-libdir IVAS_1.98.0.tar.gz >IVAS.Rcheck\00install.out 2>&1 && cp IVAS.Rcheck\00install.out IVAS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IVAS.buildbin-libdir --install="check:IVAS-install.out" --force-multiarch --no-vignettes --timings IVAS_1.98.0.tar.gz
StartedAt: 2018-04-12 00:57:12 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:03:13 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 361.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: IVAS.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   rm -rf IVAS.buildbin-libdir IVAS.Rcheck && mkdir IVAS.buildbin-libdir IVAS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IVAS.buildbin-libdir IVAS_1.98.0.tar.gz >IVAS.Rcheck\00install.out 2>&1 && cp IVAS.Rcheck\00install.out IVAS-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IVAS.buildbin-libdir --install="check:IVAS-install.out" --force-multiarch --no-vignettes --timings IVAS_1.98.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IVAS.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IVAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IVAS' version '1.98.0'
* 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 'IVAS' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/RatioFromFPKM.Rd:46: missing file link 'isActiveSeq'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/Splicingfinder.Rd:41: missing file link 'isActiveSeq'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/chrseparate.Rd:31: missing file link 'isActiveSeq'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/findAlternative.Rd:44: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/findAlternative.Rd:45: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/findOversnp.Rd:29: missing file link 'findOverlaps'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IVAS.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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ASdb-class  9.72   0.18    9.90
saveBplot   7.14   0.01    7.19
sQTLsFinder 6.77   0.03    6.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ASdb-class    14.12   0.04   14.16
saveBplot      9.88   0.06   10.56
sQTLsFinder    8.57   0.03    8.61
CalSigSNP      7.52   0.04    7.58
RatioFromFPKM  5.03   0.00    5.03
* 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
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/IVAS.Rcheck/00check.log'
for details.

Installation output

IVAS.Rcheck/00install.out


install for i386

* installing *source* package 'IVAS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'IVAS'
    finding HTML links ... done
    ASdb-class                              html  
    CalSigSNP                               html  
    IVAS-deprecated                         html  
    IVAS-package                            html  
    MsqtlFinder                             html  
    RatioFromFPKM                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/RatioFromFPKM.Rd:46: missing file link 'isActiveSeq'
    Splicingfinder                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/Splicingfinder.Rd:41: missing file link 'isActiveSeq'
    calSignificant                          html  
    chrseparate                             html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/chrseparate.Rd:31: missing file link 'isActiveSeq'
    findAlternative                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/findAlternative.Rd:44: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/findAlternative.Rd:45: missing file link 'IRanges'
    findOversnp                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpobGnRV/R.INSTALL3f46dd3f2f/IVAS/man/findOversnp.Rd:29: missing file link 'findOverlaps'
    sQTLsFinder                             html  
    sampleexp                               html  
    samplesnp                               html  
    samplesnplocus                          html  
    saveBplot                               html  
    sqtlfinder                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'IVAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IVAS' as IVAS_1.98.0.zip
* DONE (IVAS)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

IVAS.Rcheck/examples_i386/IVAS-Ex.timings

nameusersystemelapsed
ASdb-class9.720.189.90
CalSigSNP4.520.054.57
RatioFromFPKM4.000.024.01
Splicingfinder2.860.012.88
chrseparate0.070.000.08
findAlternative0.470.000.46
findOversnp0.440.020.46
sQTLsFinder6.770.036.79
sampleexp0.010.000.02
samplesnp000
samplesnplocus000
saveBplot7.140.017.19

IVAS.Rcheck/examples_x64/IVAS-Ex.timings

nameusersystemelapsed
ASdb-class14.12 0.0414.16
CalSigSNP7.520.047.58
RatioFromFPKM5.030.005.03
Splicingfinder4.040.024.05
chrseparate0.100.000.11
findAlternative0.570.030.59
findOversnp0.580.000.58
sQTLsFinder8.570.038.61
sampleexp000
samplesnp0.000.020.02
samplesnplocus000
saveBplot 9.88 0.0610.56