Package: IVAS

Version: 2.6.0

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_2.6.0.tar.gz

StartedAt: 2020-04-15 03:19:40 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:25:13 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 333.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IVAS.Rcheck

Warnings: 1

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### Running command:
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###   /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_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/IVAS.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.6.0’
* 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 ‘/Users/biocbuild/bbs-3.10-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
saveBplot     13.879  0.151  14.145
ASdb-class    13.697  0.278  14.058
sQTLsFinder   12.287  0.130  12.507
RatioFromFPKM  5.646  0.075   5.756
CalSigSNP      5.013  0.060   5.108
* 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-3.10-bioc/meat/IVAS.Rcheck/00check.log’
for details.

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### Running command:
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###   /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)

name	user	system	elapsed
ASdb-class	13.697	0.278	14.058
CalSigSNP	5.013	0.060	5.108
RatioFromFPKM	5.646	0.075	5.756
Splicingfinder	3.844	0.049	3.907
chrseparate	0.100	0.001	0.102
findAlternative	0.557	0.005	0.563
findOversnp	0.582	0.008	0.595
sQTLsFinder	12.287	0.130	12.507
sampleexp	0.006	0.002	0.008
samplesnp	0.003	0.001	0.005
samplesnplocus	0.002	0.002	0.003
saveBplot	13.879	0.151	14.145