Back to Multiple platform build/check report for BioC 3.6
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for anamiR on veracruz1

This page was generated on 2018-04-12 13:43:51 -0400 (Thu, 12 Apr 2018).

Package 43/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anamiR 1.6.1
Ti-Tai Wang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/anamiR
Branch: RELEASE_3_6
Last Commit: 64d53be
Last Changed Date: 2017-11-25 05:46:36 -0400 (Sat, 25 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: anamiR
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings anamiR_1.6.1.tar.gz
StartedAt: 2018-04-12 00:18:58 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:39:50 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 1252.2 seconds
RetCode: 0
Status:  OK 
CheckDir: anamiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings anamiR_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/anamiR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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       1.5Mb
    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         11.871  0.199 236.332
enrichment        4.690  0.807 656.590
heat_vis          1.681  0.016   7.550
database_support  1.175  0.012  37.838
miR_converter     0.034  0.002   5.771
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/anamiR.Rcheck/00check.log’
for details.



Installation output

anamiR.Rcheck/00install.out

* 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)

Tests output


Example timings

anamiR.Rcheck/anamiR-Ex.timings

nameusersystemelapsed
GSEA_ana1.9460.0492.015
GSEA_res 11.871 0.199236.332
database_support 1.175 0.01237.838
differExp_continuous0.0300.0010.032
differExp_discrete0.0290.0010.031
enrichment 4.690 0.807656.590
heat_vis1.6810.0167.550
miR_converter0.0340.0025.771
multi_Differ0.0120.0010.013
negative_cor0.9550.0050.979
normalization0.0160.0050.024