| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:36 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRSM.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1232/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miRSM 1.19.0 (landing page) Junpeng Zhang
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: miRSM |
| Version: 1.19.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings miRSM_1.19.0.tar.gz |
| StartedAt: 2023-06-06 02:15:32 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 02:24:50 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 557.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRSM.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings miRSM_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/miRSM.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘miRSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRSM’ version ‘1.19.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘miRSM’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 loading without being on the library search path ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
module_CEA 7.603 0.320 7.934
module_Coexpress 5.908 0.267 6.184
module_miRtarget 5.848 0.060 5.919
module_GFA 4.908 0.204 5.118
* 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 ...
‘miRSM.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/miRSM.Rcheck/00check.log’
for details.
miRSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL miRSM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘miRSM’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c complex.c -o complex.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o miRSM.so complex.o registerDynamicSymbol.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-miRSM/00new/miRSM/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’ Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ 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 ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’ Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ 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’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’ Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ 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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
> library(miRSM)
+----------------------------+
|............................|
|............................|
|..............########......| ####### # ###### ### #
|..............########......| # # # # # # # #
|.....####.....########......| # # # # # # # #
|.....####.....########......| ##### # # ###### # # #
|.....####...................| # ####### # # # #######
|.....####...........###.....| # # # # # # # #
|....................###.....| # # # ###### ### # #
|....................###.....|
|............................|
+----------------------------+
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 2.47.0
Warning messages:
1: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE'
2: replacing previous import 'Biobase::combine' by 'dplyr::combine' 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
21.182 0.821 22.026
miRSM.Rcheck/miRSM-Ex.timings
| name | user | system | elapsed | |
| cor_binary | 0.424 | 0.012 | 0.437 | |
| miRSM | 0.257 | 0.004 | 0.262 | |
| module_CEA | 7.603 | 0.320 | 7.934 | |
| module_Coexpress | 5.908 | 0.267 | 6.184 | |
| module_FA | 0 | 0 | 0 | |
| module_GFA | 4.908 | 0.204 | 5.118 | |
| module_NMF | 4.450 | 0.289 | 4.743 | |
| module_ProNet | 0.172 | 0.004 | 0.176 | |
| module_Validate | 4.630 | 0.128 | 4.766 | |
| module_WGCNA | 2.681 | 0.008 | 2.693 | |
| module_biclust | 0.504 | 0.004 | 0.509 | |
| module_clust | 0.141 | 0.000 | 0.142 | |
| module_igraph | 0.135 | 0.004 | 0.140 | |
| module_miRdistribute | 4.652 | 0.032 | 4.692 | |
| module_miRsponge | 4.623 | 0.024 | 4.656 | |
| module_miRtarget | 5.848 | 0.060 | 5.919 | |
| share_miRs | 4.620 | 0.103 | 4.736 | |