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This page was generated on 2024-06-18 17:59 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1291/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRSM 2.0.0  (landing page)
Junpeng Zhang
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/miRSM
git_branch: RELEASE_3_19
git_last_commit: d3b3055
git_last_commit_date: 2024-04-30 11:08:44 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for miRSM on palomino3

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.

raw results


Summary

Package: miRSM
Version: 2.0.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRSM.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings miRSM_2.0.0.tar.gz
StartedAt: 2024-06-17 06:56:17 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 07:08:31 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 733.5 seconds
RetCode: 0
Status:   OK  
CheckDir: miRSM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRSM.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings miRSM_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/miRSM.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 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 '2.0.0'
* 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) 13.2.0'
* 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 code 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 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 ... NOTE
checkRd: (-1) module_GFA.Rd:47: Lost braces
    47 | Bunte K, Lepp\'{a}aho E, Saarinen I, Kaski S. 
       |                ^
checkRd: (-1) module_GFA.Rd:50: Lost braces
    50 | Lepp\'{a}aho E, Ammad-ud-din M, Kaski S. GFA: 
       |       ^
checkRd: (-1) module_biclust.Rd:54: Lost braces
    54 | Preli\'{c} A, Bleuler S, Zimmermann P, Wille A, 
       |        ^
checkRd: (-1) module_biclust.Rd:55: Lost braces
    55 | B\'{u}hlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E. 
       |    ^
checkRd: (-1) module_biclust.Rd:80: Lost braces
    80 | Talloen W, Bijnens L, G\'{o}hlmann HW, Shkedy Z, Clevert DA. 
       |                          ^
* 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-3.19-bioc/R/library/miRSM/libs/x64/miRSM.dll':
  Found '_exit', possibly from '_exit' (C)
  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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
diff_module 8.37   1.23    9.72
miRSM_SS    6.83   0.05    6.88
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/miRSM.Rcheck/00check.log'
for details.


Installation output

miRSM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL miRSM
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'miRSM' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c complex.c -o complex.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-miRSM/00new/miRSM/libs/x64
** 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
** 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 version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  15.43   14.06   29.59 

Example timings

miRSM.Rcheck/miRSM-Ex.timings

nameusersystemelapsed
cor_binary1.440.021.46
diff_module8.371.239.72
miRSM0.170.020.19
miRSM_SS6.830.056.88
module_CEA2.910.082.98
module_Coexpress2.650.072.73
module_FA000
module_GFA3.580.223.80
module_NMF2.780.243.05
module_ProNet0.190.000.19
module_Validate2.530.062.58
module_WGCNA1.950.021.97
module_biclust0.370.030.40
module_clust0.100.010.11
module_group_sim3.201.024.27
module_igraph0.110.000.11
module_miRdistribute3.090.053.14
module_miRsponge2.910.032.94
module_miRtarget3.130.043.18
share_miRs2.950.032.99