Package: conumee

Version: 1.12.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.12.0.tar.gz

StartedAt: 2018-04-11 22:31:42 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:04:14 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 1952.3 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/conumee.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
CNV.analysis-class  99.704  0.640 100.717
CNV.detailplot_wrap 80.960  0.344  81.439
CNV.genomeplot      80.400  0.372  80.826
CNV.detailplot      79.012  0.392  79.472
CNV.write           77.968  0.536  78.602
CNV.segment         69.468  0.116  69.626
CNV.bin             48.612  0.208  48.868
CNV.fit             48.688  0.072  48.808
CNV.anno-class      42.248  0.008  42.283
CNV.detail          40.428  0.252  40.711
CNV.create_anno     39.928  0.036  39.990
read.450k.url        8.580  0.264  23.067
* 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-3.6-bioc/meat/conumee.Rcheck/00check.log’
for details.

* installing *source* package ‘conumee’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (conumee)

name	user	system	elapsed
CNV.analysis-class	99.704	0.640	100.717
CNV.anno-class	42.248	0.008	42.283
CNV.bin	48.612	0.208	48.868
CNV.create_anno	39.928	0.036	39.990
CNV.data-class	2.648	0.056	2.708
CNV.detail	40.428	0.252	40.711
CNV.detailplot	79.012	0.392	79.472
CNV.detailplot_wrap	80.960	0.344	81.439
CNV.fit	48.688	0.072	48.808
CNV.genomeplot	80.400	0.372	80.826
CNV.load	4.044	0.064	4.111
CNV.segment	69.468	0.116	69.626
CNV.write	77.968	0.536	78.602
read.450k.url	8.580	0.264	23.067