Package: conumee

Version: 1.18.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings conumee_1.18.0.tar.gz

StartedAt: 2019-10-16 00:46:42 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:21:32 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 2089.7 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.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:conumee.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings conumee_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/conumee.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ version ‘1.18.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘conumee’ 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CNV.load,GenomicRatioSet: no visible global function definition for
  ‘assays’
CNV.load,matrix: no visible binding for global variable ‘anno’
Undefined global functions or variables:
  anno assays
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
CNV.detailplot      98.883  0.376  99.546
CNV.detailplot_wrap 98.368  0.472  98.873
CNV.genomeplot      89.682  0.424  91.329
CNV.write           86.768  0.711  87.555
CNV.analysis-class  85.578  1.153  87.080
CNV.segment         84.968  0.180  85.188
CNV.detail          49.994  0.153  50.206
CNV.bin             49.359  0.112  49.476
CNV.fit             48.852  0.151  49.755
CNV.create_anno     40.201  0.008  40.214
CNV.anno-class      38.377  0.049  38.449
read.450k.url        8.717  0.243  16.996
* 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/conumee.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 conumee
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘conumee’ ...
** using staged installation
** R
** data
** 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 (conumee)

name	user	system	elapsed
CNV.analysis-class	85.578	1.153	87.080
CNV.anno-class	38.377	0.049	38.449
CNV.bin	49.359	0.112	49.476
CNV.create_anno	40.201	0.008	40.214
CNV.data-class	3.899	0.012	3.915
CNV.detail	49.994	0.153	50.206
CNV.detailplot	98.883	0.376	99.546
CNV.detailplot_wrap	98.368	0.472	98.873
CNV.fit	48.852	0.151	49.755
CNV.genomeplot	89.682	0.424	91.329
CNV.load	3.653	0.159	3.813
CNV.segment	84.968	0.180	85.188
CNV.write	86.768	0.711	87.555
read.450k.url	8.717	0.243	16.996