Package: edge

Version: 2.12.2

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:edge.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings edge_2.12.2.tar.gz

StartedAt: 2018-10-16 00:04:36 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:06:46 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 130.8 seconds

RetCode: 0

Status:  OK

CheckDir: edge.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:edge.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings edge_2.12.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/edge.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.12.2’
* 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
apply_snm 9.844  0.108   9.957
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/edge.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL edge
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘edge’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-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-3.7-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);
     ^
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o edge.so edge-init.o edgeKLODP.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/edge/libs
** 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 (edge)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, 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

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 
  6.960   0.192   7.154 

name	user	system	elapsed
apply_jackstraw	1.384	0.024	1.411
apply_qvalue	0.504	0.000	0.504
apply_snm	9.844	0.108	9.957
apply_sva	1.868	0.020	1.890
betaCoef	0.248	0.004	0.251
build_models	0.256	0.000	0.256
build_study	0.244	0.000	0.242
deSet	0.524	0.000	0.525
edge	0.004	0.000	0.000
endotoxin	0.696	0.000	0.698
fitFull	0.256	0.000	0.257
fitNull	0.276	0.004	0.283
fit_models	0.276	0.004	0.282
fullMatrix	0.260	0.000	0.261
fullModel	0.436	0.000	0.435
gibson	0.648	0.004	0.653
individual	0.248	0.000	0.249
kidney	0.756	0.000	0.757
kl_clust	0.352	0.000	0.354
lrt	0.808	0.000	0.809
nullMatrix	0.240	0.000	0.241
nullModel	0.552	0.000	0.555
odp	1.272	0.000	1.272
qvalueObj	0.792	0.000	0.795
resFull	0.252	0.000	0.252
resNull	0.288	0.000	0.286
sType	0.256	0.000	0.257
show	0.736	0.000	0.735
summary	0.724	0.008	0.731