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CHECK report for gCMAP on merida1

This page was generated on 2019-04-16 11:56:32 -0400 (Tue, 16 Apr 2019).

Package 578/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCMAP 1.26.0
Thomas Sandmann
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/gCMAP
Branch: RELEASE_3_8
Last Commit: 0913280
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gCMAP
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gCMAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gCMAP_1.26.0.tar.gz
StartedAt: 2019-04-16 00:04:29 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:07:49 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 200.2 seconds
RetCode: 0
Status:  OK 
CheckDir: gCMAP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gCMAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gCMAP_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/gCMAP.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCMAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCMAP’ version ‘1.26.0’
* 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 ‘gCMAP’ can be installed ... 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘bigmemory’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  25.562  3.458   6.351
romer_score-methods  5.649  0.931   6.230
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/gCMAP.Rcheck/00check.log’
for details.



Installation output

gCMAP.Rcheck/00install.out

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

Tests output

gCMAP.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("gCMAP") || stop("unable to load gCMAP")
Loading required package: gCMAP
Loading required package: GSEABase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA


Attaching package: 'gCMAP'

The following object is masked from 'package:IRanges':

    members

[1] TRUE
> BiocGenerics:::testPackage("gCMAP")
Loading required package: bigmemory
Loading required package: bigmemory
Design is based on 'predictor' parameter.
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory


eSets 'x' and 'y' share 500 common features.

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Loading required package: bigmemory
Design is based on 'predictor' parameter.
Loading required package: bigmemory
Loading required package: bigmemory
Design is based on 'predictor' parameter.
The following factor(s) will be ignored: score
Using type as factor of interest.
Loading required package: bigmemory
Loading required package: bigmemory


RUNIT TEST PROTOCOL -- Tue Apr 16 00:07:43 2019 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gCMAP RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 32.114   8.710  25.299 

Example timings

gCMAP.Rcheck/gCMAP-Ex.timings

nameusersystemelapsed
CMAPCollection-class1.1070.4591.054
CMAPResults-class2.0560.1882.261
KEGG2cmap000
SignedGeneSet-class0.0190.0000.019
annotate_eset_list0.1020.0070.113
camera_score-methods1.0970.4951.104
center_eSet0.0340.0050.040
connectivity_score-methods0.8540.5630.887
eSetOnDisk1.1410.1481.294
eset_instances0.0550.0040.059
featureScores-methods0.6120.2840.586
fisher_score-methods0.6810.4490.705
gCMAPData-dataset0.5050.3260.503
geneIndex-methods0.3830.1800.340
generate_gCMAP_NChannelSet0.1560.0230.179
gsealm_jg_score-methods0.5500.3160.554
gsealm_score-methods2.3160.2892.387
induceCMAPCollection-methods0.3240.1890.290
mapNmerge0.0010.0000.001
memorize0.9130.1491.073
mergeCMAPs0.1300.0040.134
mgsa_score-methods25.562 3.458 6.351
minSetSize-methods0.8020.3040.393
mroast_score-methods0.8360.3170.872
romer_score-methods5.6490.9316.230
signedRankSumTest0.0030.0000.004
splitPerturbations0.0720.0090.081
wilcox_score-methods0.5730.4890.674