Package: conumee

Version: 1.17.0

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_1.17.0.tar.gz

StartedAt: 2019-04-08 23:41:36 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-09 00:15:33 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 2036.7 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_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/conumee.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 ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ version ‘1.17.0’
* 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.genomeplot      98.776  0.451  99.364
CNV.detailplot      90.053  0.488  90.727
CNV.detailplot_wrap 85.542  0.512  86.129
CNV.segment         85.126  0.040  85.227
CNV.write           80.789  0.452  81.275
CNV.analysis-class  78.329  1.000  79.679
CNV.fit             58.387  0.028  59.523
CNV.bin             48.475  0.264  48.755
CNV.detail          42.345  0.112  42.463
CNV.create_anno     40.981  0.096  41.110
CNV.anno-class      36.985  0.016  37.013
read.450k.url        9.295  0.236  16.691
* 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	78.329	1.000	79.679
CNV.anno-class	36.985	0.016	37.013
CNV.bin	48.475	0.264	48.755
CNV.create_anno	40.981	0.096	41.110
CNV.data-class	3.303	0.016	3.319
CNV.detail	42.345	0.112	42.463
CNV.detailplot	90.053	0.488	90.727
CNV.detailplot_wrap	85.542	0.512	86.129
CNV.fit	58.387	0.028	59.523
CNV.genomeplot	98.776	0.451	99.364
CNV.load	3.272	0.063	3.334
CNV.segment	85.126	0.040	85.227
CNV.write	80.789	0.452	81.275
read.450k.url	9.295	0.236	16.691