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CHECK report for anamiR on merida2

This page was generated on 2018-10-17 08:57:19 -0400 (Wed, 17 Oct 2018).

Package 44/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anamiR 1.8.0
Ti-Tai Wang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/anamiR
Branch: RELEASE_3_7
Last Commit: 6d7c434
Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  TIMEOUT  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: anamiR
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:anamiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings anamiR_1.8.0.tar.gz
StartedAt: 2018-10-16 19:50:24 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:07:24 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 1019.4 seconds
RetCode: 0
Status:  OK 
CheckDir: anamiR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:anamiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings anamiR_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/anamiR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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 ... 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      1.7Mb
    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 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         11.889  0.242 165.189
enrichment        5.861  1.068 483.089
heat_vis          2.129  0.042   6.495
database_support  1.252  0.016  29.198
* 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-3.7-bioc/meat/anamiR.Rcheck/00check.log’
for details.



Installation output

anamiR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL anamiR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘anamiR’ ...
** 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
* DONE (anamiR)

Tests output


Example timings

anamiR.Rcheck/anamiR-Ex.timings

nameusersystemelapsed
GSEA_ana1.5841.1801.112
GSEA_res 11.889 0.242165.189
database_support 1.252 0.01629.198
differExp_continuous0.0550.0020.056
differExp_discrete0.0480.0000.049
enrichment 5.861 1.068483.089
heat_vis2.1290.0426.495
miR_converter0.0700.0024.448
multi_Differ0.0170.0010.018
negative_cor1.3250.0041.335
normalization0.0200.0070.027