John D. Storey
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/edge |
| Branch: RELEASE_3_6 |
| Last Commit: 09df4b0 |
| Last Changed Date: 2017-10-30 12:40:51 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:41 -0400 (Thu, 12 Apr 2018).
| Package 409/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| edge 2.10.0 John D. Storey
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: edge |
| Version: 2.10.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings edge_2.10.0.tar.gz |
| StartedAt: 2018-04-11 23:08:21 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:10:51 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 150.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: edge.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings edge_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/edge.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘edge’ version ‘2.10.0’
* 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 ‘edge’ 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 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
build_study: no visible global function definition for ‘as.formula’
createSet: no visible global function definition for ‘model.matrix’
deSetCheck: no visible global function definition for ‘model.matrix’
fitFDist: no visible global function definition for ‘median’
fitFDist: no visible global function definition for ‘lm.fit’
fitFDist: no visible global function definition for ‘predict’
fit_wmodels: no visible global function definition for ‘model.matrix’
fit_wmodels: no visible global function definition for ‘lm.wfit’
null: no visible global function definition for ‘model.matrix’
apply_sva,deSet: no visible global function definition for ‘as.formula’
apply_sva,deSet: no visible global function definition for ‘terms’
fit_models,deSet: no visible global function definition for
‘model.matrix’
fullModel<-,deSet: no visible global function definition for
‘model.matrix’
lrt,deSet-deFit: no visible global function definition for ‘pf’
nullModel<-,deSet: no visible global function definition for
‘model.matrix’
Undefined global functions or variables:
as.formula lm.fit lm.wfit median model.matrix pf predict terms
Consider adding
importFrom("stats", "as.formula", "lm.fit", "lm.wfit", "median",
"model.matrix", "pf", "predict", "terms")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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
apply_snm 11.948 0.136 12.115
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/edge.Rcheck/00check.log’
for details.
edge.Rcheck/00install.out
* installing *source* package ‘edge’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c edge-init.c -o edge-init.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c edgeKLODP.c -o edgeKLODP.o
edgeKLODP.c: In function ‘odpScoreCluster’:
edgeKLODP.c:65:5: warning: ‘middle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
free_vector(middle, 0, *p - 1);
^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o edge.so edge-init.o edgeKLODP.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/edge.Rcheck/edge/libs
** 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 (edge)
edge.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> library(testthat)
> library(edge)
Loading required package: Biobase
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, cbind, colMeans, colSums, colnames, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("edge")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 29 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
7.856 0.116 7.972
edge.Rcheck/edge-Ex.timings
| name | user | system | elapsed | |
| apply_jackstraw | 1.964 | 0.020 | 1.985 | |
| apply_qvalue | 0.888 | 0.000 | 0.886 | |
| apply_snm | 11.948 | 0.136 | 12.115 | |
| apply_sva | 2.276 | 0.020 | 2.298 | |
| betaCoef | 0.300 | 0.000 | 0.298 | |
| build_models | 0.304 | 0.004 | 0.307 | |
| build_study | 0.284 | 0.000 | 0.283 | |
| deSet | 0.564 | 0.000 | 0.565 | |
| edge | 0.004 | 0.000 | 0.000 | |
| endotoxin | 0.980 | 0.004 | 0.987 | |
| fitFull | 0.312 | 0.000 | 0.311 | |
| fitNull | 0.3 | 0.0 | 0.3 | |
| fit_models | 0.336 | 0.004 | 0.341 | |
| fullMatrix | 0.308 | 0.000 | 0.307 | |
| fullModel | 0.508 | 0.000 | 0.510 | |
| gibson | 0.708 | 0.008 | 0.720 | |
| individual | 0.316 | 0.000 | 0.317 | |
| kidney | 0.896 | 0.004 | 0.902 | |
| kl_clust | 0.404 | 0.000 | 0.407 | |
| lrt | 0.860 | 0.004 | 0.866 | |
| nullMatrix | 0.332 | 0.000 | 0.332 | |
| nullModel | 0.712 | 0.004 | 0.717 | |
| odp | 1.440 | 0.000 | 1.442 | |
| qvalueObj | 0.876 | 0.004 | 0.878 | |
| resFull | 0.584 | 0.000 | 0.584 | |
| resNull | 0.312 | 0.000 | 0.310 | |
| sType | 0.304 | 0.000 | 0.305 | |
| show | 0.868 | 0.000 | 0.871 | |
| summary | 0.800 | 0.000 | 0.803 | |