BioC 3.2: CHECK report for conumee on zin1

Package: conumee

Version: 1.1.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.1.0.tar.gz

StartedAt: 2015-08-23 22:54:22 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:11:28 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 1025.5 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/conumee.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.1.0’
* 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 ... [18s/18s] 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,matrix : .local: no visible binding for global variable ‘anno’
* 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 ... [14m/14m] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNV.detailplot_wrap 103.004  0.344 103.470
CNV.analysis-class  101.928  0.759 103.080
CNV.detailplot       99.455  0.388 100.594
CNV.genomeplot       99.110  0.479  99.721
CNV.write            98.898  0.296  99.203
CNV.segment          87.919  0.021  87.975
CNV.bin              47.186  0.135  47.470
CNV.detail           46.015  0.032  46.195
CNV.fit              44.106  0.016  44.140
CNV.create_anno      42.568  0.020  42.731
CNV.anno-class       41.743  0.024  41.823
read.450k.url         4.600  0.084  12.967
* 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-3.2-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	101.928	0.759	103.080
CNV.anno-class	41.743	0.024	41.823
CNV.bin	47.186	0.135	47.470
CNV.create_anno	42.568	0.020	42.731
CNV.data-class	1.680	0.048	1.732
CNV.detail	46.015	0.032	46.195
CNV.detailplot	99.455	0.388	100.594
CNV.detailplot_wrap	103.004	0.344	103.470
CNV.fit	44.106	0.016	44.140
CNV.genomeplot	99.110	0.479	99.721
CNV.load	1.867	0.008	1.877
CNV.segment	87.919	0.021	87.975
CNV.write	98.898	0.296	99.203
read.450k.url	4.600	0.084	12.967