Thomas Sandmann
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/gCMAP |
| Branch: RELEASE_3_9 |
| Last Commit: 638e459 |
| Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:50:35 -0400 (Wed, 16 Oct 2019).
| Package 610/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gCMAP 1.28.0 Thomas Sandmann
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... | ||||||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| Package: gCMAP |
| Version: 1.28.0 |
| 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_1.28.0.tar.gz |
| StartedAt: 2019-10-16 02:57:57 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:03:01 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 303.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gCMAP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gCMAP.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.28.0’
* 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 29.498 1.425 8.621
romer_score-methods 8.752 2.103 10.224
CMAPCollection-class 3.255 3.018 3.539
gsealm_score-methods 4.645 1.096 5.012
* 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-3.9-bioc/meat/gCMAP.Rcheck/00check.log’
for details.
gCMAP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gCMAP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘gCMAP’ ... ** using staged installation ** 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 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 (gCMAP)
gCMAP.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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 -- Wed Oct 16 03:02:52 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
44.363 13.928 40.354
gCMAP.Rcheck/gCMAP-Ex.timings
| name | user | system | elapsed | |
| CMAPCollection-class | 3.255 | 3.018 | 3.539 | |
| CMAPResults-class | 3.159 | 0.419 | 3.578 | |
| KEGG2cmap | 0.000 | 0.001 | 0.000 | |
| SignedGeneSet-class | 0.033 | 0.007 | 0.040 | |
| annotate_eset_list | 0.120 | 0.029 | 0.149 | |
| camera_score-methods | 1.967 | 1.076 | 2.128 | |
| center_eSet | 0.056 | 0.012 | 0.068 | |
| connectivity_score-methods | 1.522 | 1.170 | 1.637 | |
| eSetOnDisk | 1.819 | 0.476 | 2.298 | |
| eset_instances | 0.057 | 0.009 | 0.067 | |
| featureScores-methods | 1.145 | 0.708 | 1.235 | |
| fisher_score-methods | 1.134 | 0.709 | 1.225 | |
| gCMAPData-dataset | 0.712 | 0.470 | 0.691 | |
| geneIndex-methods | 0.930 | 0.732 | 0.904 | |
| generate_gCMAP_NChannelSet | 0.224 | 0.054 | 0.277 | |
| gsealm_jg_score-methods | 1.202 | 0.927 | 1.313 | |
| gsealm_score-methods | 4.645 | 1.096 | 5.012 | |
| induceCMAPCollection-methods | 0.633 | 0.506 | 0.659 | |
| mapNmerge | 0.001 | 0.000 | 0.001 | |
| memorize | 1.519 | 0.499 | 2.021 | |
| mergeCMAPs | 0.145 | 0.008 | 0.153 | |
| mgsa_score-methods | 29.498 | 1.425 | 8.621 | |
| minSetSize-methods | 0.788 | 0.602 | 0.659 | |
| mroast_score-methods | 1.869 | 1.367 | 2.182 | |
| romer_score-methods | 8.752 | 2.103 | 10.224 | |
| signedRankSumTest | 0.002 | 0.001 | 0.004 | |
| splitPerturbations | 0.117 | 0.017 | 0.133 | |
| wilcox_score-methods | 0.977 | 1.077 | 1.246 | |