Package: IntEREst

Version: 1.7.3

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IntEREst_1.7.3.tar.gz

StartedAt: 2019-04-09 01:24:07 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:29:28 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 320.6 seconds

RetCode: 0

Status:  OK

CheckDir: IntEREst.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IntEREst_1.7.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IntEREst.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntEREst/DESCRIPTION’ ... OK
* this is package ‘IntEREst’ version ‘1.7.3’
* 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 ‘IntEREst’ 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
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.InterestResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateU12: no visible binding for global variable ‘query’
Undefined global functions or variables:
  query
* 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
DEXSeqIntEREst 32.777  0.128  32.926
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/IntEREst.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IntEREst
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘IntEREst’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (IntEREst)

name	user	system	elapsed
DEXSeqIntEREst	32.777	0.128	32.926
addAnnotation	0.039	0.000	0.039
annotateU12	3.272	0.024	3.550
attributes	0.051	0.000	0.051
boxplot-method	0.093	0.000	0.093
buildSsTypePwms	0	0	0
counts-method	0.102	0.000	0.102
deseqInterest	4.519	0.004	4.524
exactTestInterest	0.173	0.000	0.173
getRepeatTable	0	0	0
glmInterest	0.226	0.000	0.226
interest	1.741	0.008	1.772
interest.sequential	1.288	0.004	1.292
interestResult	0.013	0.000	0.013
interestResultIntEx	0.128	0.000	0.128
intexIndex	0.004	0.000	0.004
lfc	0.106	0.000	0.105
mergeInterestResult	0.222	0.000	0.222
plot-method	0.272	0.000	0.272
psi	1.143	0.008	1.151
qlfInterest	0.266	0.004	0.270
readInterestResults	0.04	0.00	0.04
referencePrepare	1.191	0.008	1.200
subInterestResult	0.028	0.000	0.029
treatInterest	0.179	0.004	0.182
u12Boxplot	0.068	0.000	0.067
u12BoxplotNb	0.119	0.000	0.119
u12DensityPlot	0.316	0.000	0.317
u12Index	0.007	0.000	0.007
u12NbIndex	0.067	0.000	0.066
unionRefTr	0.014	0.000	0.014
updateRowDataCol	0.031	0.000	0.031