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CHECK report for IVAS on malbec2

This page was generated on 2018-10-17 08:27:10 -0400 (Wed, 17 Oct 2018).

Package 764/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 2.0.0
Seonggyun Han
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/IVAS
Branch: RELEASE_3_7
Last Commit: 7878acf
Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: IVAS
Version: 2.0.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IVAS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IVAS_2.0.0.tar.gz
StartedAt: 2018-10-16 01:25:58 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 01:29:19 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 201.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IVAS.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IVAS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IVAS_2.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/IVAS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘2.0.0’
* 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 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 ‘/home/biocbuild/bbs-3.7-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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ASdb-class  7.608  0.140   7.756
saveBplot   7.524  0.072   7.606
sQTLsFinder 6.920  0.032   6.955
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/IVAS.Rcheck/00check.log’
for details.



Installation output

IVAS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL IVAS
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘IVAS’ ...
** 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
* DONE (IVAS)

Tests output


Example timings

IVAS.Rcheck/IVAS-Ex.timings

nameusersystemelapsed
ASdb-class7.6080.1407.756
CalSigSNP3.1760.0163.194
RatioFromFPKM4.3200.0204.344
Splicingfinder2.7840.0242.810
chrseparate0.0760.0000.077
findAlternative0.4560.0000.454
findOversnp0.480.000.48
sQTLsFinder6.9200.0326.955
sampleexp0.0040.0000.003
samplesnp0.0040.0000.003
samplesnplocus0.0040.0000.002
saveBplot7.5240.0727.606