John D. Storey
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/edge |
| git_branch: RELEASE_3_16 |
| git_last_commit: e8b67e9 |
| git_last_commit_date: 2022-11-20 15:30:22 -0400 (Sun, 20 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:32 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 594/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| edge 2.30.0 (landing page) John D. Storey
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: edge |
| Version: 2.30.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:edge.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings edge_2.30.0.tar.gz |
| StartedAt: 2023-04-11 01:07:47 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 01:11:20 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 212.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: edge.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:edge.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings edge_2.30.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/edge.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '2.30.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/edge/libs/x64/edge.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted 'edge.pdf' from 463Kb to 354Kb
consider running tools::compactPDF() on these files
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
apply_snm 10.82 0.87 11.8
* 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, 3 NOTEs
See
'F:/biocbuild/bbs-3.16-bioc/meat/edge.Rcheck/00check.log'
for details.
edge.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL edge
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'edge' ...
** using staged installation
** libs
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c edge-init.c -o edge-init.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c edgeKLODP.c -o edgeKLODP.o
edgeKLODP.c: In function 'odpScoreCluster':
edgeKLODP.c:194:27: warning: 'middle' may be used uninitialized in this function [-Wmaybe-uninitialized]
194 | free((FREE_ARG) (v + nl - NR_END));
| ~~~~~~~~^~~~~~~~~
edgeKLODP.c:11:19: note: 'middle' was declared here
11 | double *first, *middle;
| ^~~~~~
gcc -shared -s -static-libgcc -o edge.dll tmp.def edge-init.o edgeKLODP.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-edge/00new/edge/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (edge)
edge.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, aperm, 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
10.39 0.56 10.95
edge.Rcheck/edge-Ex.timings
| name | user | system | elapsed | |
| apply_qvalue | 0.78 | 0.03 | 0.81 | |
| apply_snm | 10.82 | 0.87 | 11.80 | |
| apply_sva | 2.81 | 0.16 | 2.97 | |
| betaCoef | 0.27 | 0.03 | 0.29 | |
| build_models | 0.28 | 0.03 | 0.31 | |
| build_study | 0.33 | 0.00 | 0.33 | |
| deSet | 0.61 | 0.02 | 0.63 | |
| edge | 0 | 0 | 0 | |
| endotoxin | 0.78 | 0.09 | 0.87 | |
| fitFull | 0.31 | 0.02 | 0.33 | |
| fitNull | 0.36 | 0.00 | 0.36 | |
| fit_models | 0.33 | 0.00 | 0.33 | |
| fullMatrix | 0.34 | 0.00 | 0.34 | |
| fullModel | 0.50 | 0.03 | 0.53 | |
| gibson | 0.75 | 0.05 | 0.80 | |
| individual | 0.32 | 0.01 | 0.33 | |
| kidney | 0.81 | 0.03 | 0.84 | |
| kl_clust | 0.45 | 0.05 | 0.50 | |
| lrt | 1.20 | 0.05 | 1.25 | |
| nullMatrix | 0.44 | 0.01 | 0.45 | |
| nullModel | 0.72 | 0.00 | 0.72 | |
| odp | 1.48 | 0.27 | 1.75 | |
| qvalueObj | 0.84 | 0.06 | 0.91 | |
| resFull | 0.32 | 0.00 | 0.31 | |
| resNull | 0.45 | 0.00 | 0.45 | |
| sType | 0.3 | 0.0 | 0.3 | |
| show | 0.95 | 0.11 | 1.06 | |
| summary | 1.01 | 0.08 | 1.09 | |