| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:39 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 miRSM package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1206/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miRSM 1.17.0 (landing page) Junpeng Zhang
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: miRSM |
| Version: 1.17.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRSM.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings miRSM_1.17.0.tar.gz |
| StartedAt: 2022-12-29 01:27:21 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 01:32:42 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 320.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRSM.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRSM.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings miRSM_1.17.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/miRSM.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'miRSM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miRSM' version '1.17.0'
* package encoding: UTF-8
* 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 'miRSM' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 ... NOTE
Namespace in Imports field not imported from: 'org.Hs.eg.db'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/miRSM/libs/x64/miRSM.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 nor [v]sprintf. 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'test_miRSM.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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/miRSM.Rcheck/00check.log'
for details.
miRSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL miRSM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'miRSM' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c complex.c -o complex.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -s -static-libgcc -o miRSM.dll tmp.def complex.o registerDynamicSymbol.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-miRSM/00new/miRSM/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE' Warning: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE' Warning: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE' Warning: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE' Warning: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE' Warning: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE' Warning: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE' Warning: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE' Warning: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE' Warning: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE' Warning: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE' ** testing if installed package can be loaded from final location Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE' Warning: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE' Warning: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE' Warning: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE' Warning: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE' Warning: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE' ** testing if installed package keeps a record of temporary installation path * DONE (miRSM)
miRSM.Rcheck/tests/test_miRSM.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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(GSEABase)
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
> library(miRSM)
+----------------------------+
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|..............########......| ####### # ###### ### #
|..............########......| # # # # # # # #
|.....####.....########......| # # # # # # # #
|.....####.....########......| ##### # # ###### # # #
|.....####...................| # ####### # # # #######
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|....................###.....| # # # ###### ### # #
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+----------------------------+
Citation: S. Hochreiter et al.,
FABIA: Factor Analysis for Bicluster Acquisition,
Bioinformatics 26(12):1520-1527, 2010.
BibTex: enter 'toBibtex(citation("fabia"))'
Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html
FABIA Package Version 2.45.0
Warning messages:
1: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE'
2: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE'
3: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE'
4: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE'
5: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE'
6: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE'
7: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE'
>
> # Load datasets
> data(BRCASampleData)
>
> # Identify gene co-expression modules using igraph method
> modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)],
+ mRExp[, seq_len(10)])
>
>
> test_that("Test miRSM", {
+ expect_equal(geneIds(module_igraph(ceRExp[, seq_len(10)],
+ mRExp[, seq_len(10)])), geneIds(modulegenes_igraph))
+ })
Test passed 🎉
>
> proc.time()
user system elapsed
12.95 1.39 14.20
miRSM.Rcheck/miRSM-Ex.timings
| name | user | system | elapsed | |
| cor_binary | 0.18 | 0.03 | 0.21 | |
| miRSM | 0.17 | 0.00 | 0.17 | |
| module_CEA | 3.68 | 0.00 | 3.68 | |
| module_Coexpress | 2.89 | 0.06 | 2.95 | |
| module_FA | 0 | 0 | 0 | |
| module_GFA | 2.64 | 0.08 | 2.72 | |
| module_NMF | 2.37 | 0.06 | 2.44 | |
| module_ProNet | 0.11 | 0.02 | 0.12 | |
| module_Validate | 2.24 | 0.04 | 2.28 | |
| module_WGCNA | 1.53 | 0.01 | 1.54 | |
| module_biclust | 0.36 | 0.00 | 0.36 | |
| module_clust | 0.11 | 0.00 | 0.11 | |
| module_igraph | 0.09 | 0.00 | 0.10 | |
| module_miRdistribute | 2.20 | 0.05 | 2.25 | |
| module_miRsponge | 2.28 | 0.03 | 2.31 | |
| module_miRtarget | 2.27 | 0.00 | 2.26 | |
| share_miRs | 2.21 | 0.02 | 2.24 | |