Package: conumee

Version: 1.20.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings conumee_1.20.0.tar.gz

StartedAt: 2020-04-15 02:59:07 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:33:54 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 2087.0 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings conumee_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/conumee.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.20.0’
* 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_wrap 96.572  0.660  97.474
CNV.genomeplot      96.468  0.420  97.731
CNV.detailplot      89.160  0.552  90.026
CNV.write           88.572  0.684  89.635
CNV.analysis-class  80.588  0.996  82.006
CNV.segment         79.460  0.020  79.702
CNV.fit             49.604  0.164  49.857
CNV.bin             49.312  0.068  49.548
CNV.detail          48.492  0.216  48.833
CNV.create_anno     42.048  0.016  42.176
CNV.anno-class      41.344  0.040  41.459
read.450k.url       10.364  0.176  20.700
* 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-3.10-bioc/meat/conumee.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL conumee
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* installing to library ‘/home/biocbuild/bbs-3.10-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	80.588	0.996	82.006
CNV.anno-class	41.344	0.040	41.459
CNV.bin	49.312	0.068	49.548
CNV.create_anno	42.048	0.016	42.176
CNV.data-class	3.496	0.068	3.567
CNV.detail	48.492	0.216	48.833
CNV.detailplot	89.160	0.552	90.026
CNV.detailplot_wrap	96.572	0.660	97.474
CNV.fit	49.604	0.164	49.857
CNV.genomeplot	96.468	0.420	97.731
CNV.load	3.344	0.016	3.367
CNV.segment	79.460	0.020	79.702
CNV.write	88.572	0.684	89.635
read.450k.url	10.364	0.176	20.700