Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-01 17:17:24 -0500 (Wed, 01 Dec 2021).

CHECK results for edge on nebbiolo2

To the developers/maintainers of the edge package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/edge.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 565/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
edge 2.26.0  (landing page)
John D. Storey , Andrew J. Bass
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/edge
git_branch: RELEASE_3_14
git_last_commit: 6eaa176
git_last_commit_date: 2021-10-26 12:20:40 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: edge
Version: 2.26.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:edge.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings edge_2.26.0.tar.gz
StartedAt: 2021-11-30 09:00:09 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 09:03:13 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 184.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: edge.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:edge.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings edge_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/edge.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.26.0’
* 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 ... 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 ... WARNING
Documented arguments not in \usage in documentation object 'show':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... 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 (user + system) or elapsed time > 5s
            user system elapsed
apply_snm 11.366  0.304   11.67
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/edge.Rcheck/00check.log’
for details.



Installation output

edge.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL edge
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘edge’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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]
   65 |     free_vector(middle, 0, *p - 1);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o edge.so edge-init.o edgeKLODP.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-edge/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (edge)

Tests output

edge.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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

Attaching package: 'BiocGenerics'

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.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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 10.468   0.335  10.789 

Example timings

edge.Rcheck/edge-Ex.timings

nameusersystemelapsed
apply_jackstraw1.7870.0441.831
apply_qvalue0.6080.0080.617
apply_snm11.366 0.30411.670
apply_sva2.0310.0162.047
betaCoef0.2640.0040.268
build_models0.2770.0120.289
build_study0.2870.0040.291
deSet0.6440.0000.644
edge000
endotoxin0.8250.0160.841
fitFull0.2920.0000.292
fitNull0.2740.0000.274
fit_models0.3040.0120.316
fullMatrix0.2740.0000.274
fullModel0.5040.0000.504
gibson0.7420.0160.758
individual0.2610.0040.265
kidney0.8280.0160.845
kl_clust0.4160.0000.416
lrt1.7260.0231.749
nullMatrix0.3010.0040.305
nullModel0.7050.0080.713
odp1.5840.0281.613
qvalueObj0.7960.0080.804
resFull0.3000.0080.307
resNull0.2970.0000.297
sType0.2780.0000.277
show0.7550.0120.766
summary0.7860.0000.786