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CHECK report for IVAS on celaya2

This page was generated on 2019-04-09 13:13:25 -0400 (Tue, 09 Apr 2019).

Package 832/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 2.3.1
Seonggyun Han
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/IVAS
Branch: master
Last Commit: 5121735
Last Changed Date: 2019-01-04 13:36:40 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: IVAS
Version: 2.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IVAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IVAS_2.3.1.tar.gz
StartedAt: 2019-04-09 02:59:58 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:06:15 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 377.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IVAS.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IVAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IVAS_2.3.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IVAS.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IVAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IVAS’ version ‘2.3.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘IVAS’ can be installed ... WARNING
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/IVAS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
ASdb-class    13.498  0.436  14.393
saveBplot     12.523  0.232  12.798
sQTLsFinder   11.881  0.178  12.069
RatioFromFPKM  7.011  0.117   7.145
CalSigSNP      5.876  0.107   6.197
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/IVAS.Rcheck/00check.log’
for details.



Installation output

IVAS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IVAS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘IVAS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: next used in wrong context: no loop is visible 
** help
*** installing help indices
** 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
* DONE (IVAS)

Tests output


Example timings

IVAS.Rcheck/IVAS-Ex.timings

nameusersystemelapsed
ASdb-class13.498 0.43614.393
CalSigSNP5.8760.1076.197
RatioFromFPKM7.0110.1177.145
Splicingfinder4.7110.0854.804
chrseparate0.1070.0030.119
findAlternative0.5790.0100.590
findOversnp0.6890.0120.701
sQTLsFinder11.881 0.17812.069
sampleexp0.0040.0020.006
samplesnp0.0030.0020.005
samplesnplocus0.0030.0030.006
saveBplot12.523 0.23212.798