Package: anamiR

Version: 1.6.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings anamiR_1.6.1.tar.gz

StartedAt: 2018-04-11 21:25:04 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 21:43:39 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 1114.5 seconds

RetCode: 0

Status:  OK

CheckDir: anamiR.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 anamiR_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/anamiR.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 ‘anamiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘anamiR’ version ‘1.6.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘anamiR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.0Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    doc       1.4Mb
    extdata  19.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘SummarizedExperiment’
A package should be listed in only one of these fields.
* 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
GSEA_ana: no visible binding for global variable ‘msigdb.gs’
Undefined global functions or variables:
  msigdb.gs
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
GSEA_res         9.212  0.084 210.938
enrichment       5.748  0.176 587.429
heat_vis         1.544  0.000   7.044
database_support 0.932  0.000  36.681
miR_converter    0.032  0.000   5.611
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/anamiR.Rcheck/00check.log’
for details.

* installing *source* package ‘anamiR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (anamiR)

name	user	system	elapsed
GSEA_ana	2.112	0.020	2.134
GSEA_res	9.212	0.084	210.938
database_support	0.932	0.000	36.681
differExp_continuous	0.044	0.000	0.041
differExp_discrete	0.036	0.000	0.034
enrichment	5.748	0.176	587.429
heat_vis	1.544	0.000	7.044
miR_converter	0.032	0.000	5.611
multi_Differ	0.012	0.000	0.014
negative_cor	0.876	0.004	0.882
normalization	0.012	0.000	0.011