Package: ACE

Version: 1.1.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ACE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ACE_1.1.1.tar.gz

StartedAt: 2019-04-08 22:36:19 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 22:39:36 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 197.3 seconds

RetCode: 0

Status:  OK

CheckDir: ACE.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:ACE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ACE_1.1.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ACE.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 ‘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        13.199  0.004  13.525
squaremodelsummary 12.680  0.000  12.714
twosamplecompare    5.021  0.000   5.044
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ACE.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 ACE
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ACE’ ...
** using staged installation
** 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 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 (ACE)

name	user	system	elapsed
ACEcall	1.557	0.172	1.729
analyzegenomiclocations	0.019	0.000	0.019
compresstemplate	0.034	0.008	0.042
copyNumbersSegmented	0.771	0.016	0.787
correlationmatrix	0.068	0.000	0.069
forcesegmentsontemplate	0.279	0.000	0.279
getadjustedsegments	0.197	0.000	0.196
linkvariants	0.027	0.004	0.031
loopsquaremodel	4.747	0.023	4.777
objectsampletotemplate	0.008	0.004	0.012
postanalysisloop	0.001	0.000	0.001
runACE	0.001	0.000	0.001
singlemodel	1.416	0.000	1.418
singleplot	1.622	0.004	1.630
squaremodel	13.199	0.004	13.525
squaremodelsummary	12.680	0.000	12.714
templatefromequalsegments	0.030	0.000	0.031
twosamplecompare	5.021	0.000	5.044