Package: ACE

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ACE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ACE_1.1.1.tar.gz

StartedAt: 2019-04-08 23:07:28 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:10:43 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 194.8 seconds

RetCode: 0

Status:  OK

CheckDir: ACE.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ACE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ACE_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ACE.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ACE/DESCRIPTION’ ... OK
* this is package ‘ACE’ version ‘1.1.1’
* package encoding: UTF-8
* 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 ‘ACE’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘QDNAseq:::sdDiffTrim’
  See the note in ?`:::` about the use of this operator.
* 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
squaremodel        13.847  0.142  15.269
squaremodelsummary 12.716  0.118  12.955
loopsquaremodel     5.836  0.055   5.913
twosamplecompare    5.632  0.066   5.775
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ACE.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 ACE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ACE’ ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ACE)

name	user	system	elapsed
ACEcall	2.257	0.371	2.705
analyzegenomiclocations	0.033	0.006	0.040
compresstemplate	0.082	0.002	0.085
copyNumbersSegmented	1.203	0.044	1.250
correlationmatrix	0.132	0.003	0.136
forcesegmentsontemplate	0.501	0.009	0.513
getadjustedsegments	0.265	0.005	0.273
linkvariants	0.027	0.002	0.028
loopsquaremodel	5.836	0.055	5.913
objectsampletotemplate	0.009	0.001	0.010
postanalysisloop	0.000	0.000	0.001
runACE	0.000	0.001	0.000
singlemodel	1.433	0.070	1.594
singleplot	1.366	0.015	1.393
squaremodel	13.847	0.142	15.269
squaremodelsummary	12.716	0.118	12.955
templatefromequalsegments	0.034	0.003	0.036
twosamplecompare	5.632	0.066	5.775