Package: anamiR

Version: 1.13.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:anamiR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings anamiR_1.13.0.tar.gz

StartedAt: 2019-09-05 00:07:34 -0400 (Thu, 05 Sep 2019)

EndedAt: 2019-09-05 00:24:30 -0400 (Thu, 05 Sep 2019)

EllapsedTime: 1016.4 seconds

RetCode: 0

Status:  OK

CheckDir: anamiR.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:anamiR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings anamiR_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/anamiR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.13.0’
* package encoding: UTF-8
* 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 21.5Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata  19.6Mb
* 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
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
GSEA_res         10.536  0.192 180.200
enrichment        5.308  0.256 468.615
heat_vis          1.804  0.004   6.605
database_support  1.696  0.012  30.337
* 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/anamiR.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 anamiR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘anamiR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (anamiR)

name	user	system	elapsed
GSEA_ana	1.688	0.040	2.398
GSEA_res	10.536	0.192	180.200
database_support	1.696	0.012	30.337
differExp_continuous	0.324	0.008	0.336
differExp_discrete	0.316	0.008	0.324
enrichment	5.308	0.256	468.615
heat_vis	1.804	0.004	6.605
miR_converter	0.328	0.000	4.907
multi_Differ	0.948	0.008	0.970
negative_cor	1.492	0.004	1.497
normalization	0.016	0.000	0.030