John D. Storey
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/edge |
| Branch: RELEASE_3_7 |
| Last Commit: dfdcbff |
| Last Changed Date: 2018-08-30 08:49:43 -0400 (Thu, 30 Aug 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:27:39 -0400 (Wed, 17 Oct 2018).
| Package 433/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| edge 2.12.2 John D. Storey
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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.
edge.Rcheck/00install.out
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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)
edge.Rcheck/tests/testthat.Rout
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
edge.Rcheck/edge-Ex.timings
| 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 | |