Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-09 12:05 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 1297/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miRSM 2.5.4 (landing page) Junpeng Zhang
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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. |
Package: miRSM |
Version: 2.5.4 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings miRSM_2.5.4.tar.gz |
StartedAt: 2025-08-09 00:17:42 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 00:25:01 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 438.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: miRSM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings miRSM_2.5.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/miRSM.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘miRSM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘miRSM’ version ‘2.5.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 31 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 8.2Mb sub-directories of 1Mb or more: java 4.2Mb libs 2.9Mb * 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 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 ... NOTE layout.spencer.circle: no visible global function definition for ‘orderCommunities’ plotLinkCommGraph: no visible global function definition for ‘which.communities’ plotLinkCommGraph: no visible global function definition for ‘orderCommunities’ plotLinkCommGraph: no visible global function definition for ‘numberEdgesIn’ plotLinkCommGraph: no visible global function definition for ‘.nodePie’ plotLinkCommMembers: no visible global function definition for ‘getCommunityMatrix’ plotLinkCommSummComm: no visible global function definition for ‘LinkDensities’ plotLinkCommSummComm: no visible global function definition for ‘getCommunityConnectedness’ s4vd: no visible global function definition for ‘BiclustResult’ ssvd: no visible global function definition for ‘irlba’ ssvd: no visible global function definition for ‘%dopar%’ ssvd: no visible global function definition for ‘foreach’ ssvd: no visible global function definition for ‘thresh’ ssvdBC: no visible global function definition for ‘BiclustResult’ Undefined global functions or variables: %dopar% .nodePie BiclustResult LinkDensities foreach getCommunityConnectedness getCommunityMatrix irlba numberEdgesIn orderCommunities thresh which.communities * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... 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 8.56 0.141 8.701 miRSM_SS 6.70 0.037 6.738 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/miRSM.Rcheck/00check.log’ for details.
miRSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL miRSM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘miRSM’ ... ** this is package ‘miRSM’ version ‘2.5.4’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c OCG_algorithm.c -o OCG_algorithm.o OCG_algorithm.c: In function ‘getOCGclusters’: OCG_algorithm.c:568:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 568 | for(j=0;j<CardMax;j++) | ^~~ OCG_algorithm.c:571:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 571 | k=0; | ^ OCG_algorithm.c:445:52: warning: variable ‘flag3’ set but not used [-Wunused-but-set-variable] 445 | int NbY, Nl, Long, NewLong, cli, flag1, flag2, flag3; | ^~~~~ OCG_algorithm.c:790:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 790 | for (j=0; j<i; j++) | ^~~ OCG_algorithm.c:794:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 794 | for (k=0; k<N; k++) Clas[k]=0; | ^~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c complex.c -o complex.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c edge_duplicates.cpp -o edge_duplicates.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c linkcomm_edgesims.cpp -o linkcomm_edgesims.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c linkcomm_edgesims_all.cpp -o linkcomm_edgesims_all.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c linkcomm_functions.cpp -o linkcomm_functions.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c linkcomm_hclust.cpp -o linkcomm_hclust.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c linkcomm_init.c -o linkcomm_init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c linkcomm_linkdensities.cpp -o linkcomm_linkdensities.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c linkcommhclust_order.cpp -o linkcommhclust_order.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c read_OCG.cpp -o read_OCG.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o miRSM.so OCG_algorithm.o complex.o edge_duplicates.o linkcomm_edgesims.o linkcomm_edgesims_all.o linkcomm_functions.o linkcomm_hclust.o linkcomm_init.o linkcomm_linkdensities.o linkcommhclust_order.o read_OCG.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/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)
miRSM.Rcheck/tests/test_miRSM.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-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 14.717 0.803 15.509
miRSM.Rcheck/miRSM-Ex.timings
name | user | system | elapsed | |
cor_binary | 0.192 | 0.008 | 0.199 | |
diff_module | 8.560 | 0.141 | 8.701 | |
miRSM | 0.207 | 0.003 | 0.210 | |
miRSM_SS | 6.700 | 0.037 | 6.738 | |
module_CEA | 2.972 | 0.040 | 3.011 | |
module_Coexpress | 2.658 | 0.042 | 2.700 | |
module_FA | 0 | 0 | 0 | |
module_GFA | 3.225 | 0.126 | 3.351 | |
module_NMF | 2.970 | 0.016 | 2.983 | |
module_ProNet | 0.140 | 0.002 | 0.142 | |
module_Validate | 2.821 | 0.070 | 2.891 | |
module_WGCNA | 2.089 | 0.072 | 2.162 | |
module_biclust | 0.394 | 0.013 | 0.408 | |
module_clust | 0.119 | 0.007 | 0.127 | |
module_group_sim | 3.064 | 0.220 | 3.285 | |
module_igraph | 0.125 | 0.003 | 0.128 | |
module_miRdistribute | 3.117 | 0.160 | 3.277 | |
module_miRsponge | 2.816 | 0.088 | 2.904 | |
module_miRtarget | 3.049 | 0.039 | 3.088 | |
share_miRs | 2.774 | 0.106 | 2.881 | |