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This page was generated on 2024-02-28 11:40:22 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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

Package 1264/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRSM 1.99.5  (landing page)
Junpeng Zhang
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/miRSM
git_branch: devel
git_last_commit: d93b1a3
git_last_commit_date: 2024-02-26 09:18:31 -0500 (Mon, 26 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for miRSM on kunpeng2


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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: miRSM
Version: 1.99.5
Command: /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings miRSM_1.99.5.tar.gz
StartedAt: 2024-02-27 08:06:04 -0000 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 08:14:21 -0000 (Tue, 27 Feb 2024)
EllapsedTime: 496.8 seconds
RetCode: 0
Status:   OK  
CheckDir: miRSM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings miRSM_1.99.5.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/miRSM.Rcheck’
* using R Under development (unstable) (2024-01-16 r85812)
* using platform: aarch64-unknown-linux-gnu
* 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
* using option ‘--no-vignettes’
* checking for file ‘miRSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRSM’ version ‘1.99.5’
* 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 whether startup messages can be suppressed ... 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 ... 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
diff_module 9.565  0.088   9.666
miRSM_SS    7.687  0.056   7.755
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_miRSM.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/miRSM.Rcheck/00check.log’
for details.



Installation output

miRSM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD INSTALL miRSM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library’
* installing *source* package ‘miRSM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c complex.c -o complex.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -shared -L/home/biocbuild/R/R-devel_2024-01-16_r85812/lib -L/usr/local/lib -o miRSM.so complex.o registerDynamicSymbol.o -L/home/biocbuild/R/R-devel_2024-01-16_r85812/lib -lR
installing to /home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/00LOCK-miRSM/00new/miRSM/libs
** R
** data
** 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 (miRSM)

Tests output

miRSM.Rcheck/tests/test_miRSM.Rout


R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> suppressPackageStartupMessages(library(testthat))
> suppressPackageStartupMessages(library(GSEABase))
> suppressPackageStartupMessages(library(miRSM))
> 
> # 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 
 19.570   0.685  20.273 

Example timings

miRSM.Rcheck/miRSM-Ex.timings

nameusersystemelapsed
cor_binary0.2440.0160.259
diff_module9.5650.0889.666
miRSM0.2150.0040.220
miRSM_SS7.6870.0567.755
module_CEA3.2210.0003.226
module_Coexpress3.2840.0283.317
module_FA000
module_GFA4.3190.0484.373
module_NMF3.7710.0603.835
module_ProNet0.1620.0040.167
module_Validate3.3010.0163.323
module_WGCNA2.4190.0202.443
module_biclust0.5000.0040.505
module_clust0.1330.0040.137
module_group_sim3.5060.0003.510
module_igraph0.1350.0000.136
module_miRdistribute3.2110.0003.216
module_miRsponge3.2030.0043.209
module_miRtarget3.2810.0043.290
share_miRs3.2650.0083.278