Junpeng Zhang
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/miRspongeR |
| git_branch: devel |
| git_last_commit: 84d7ec9 |
| git_last_commit_date: 2025-06-18 04:39:45 -0400 (Wed, 18 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:02 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 1294/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miRspongeR 2.13.2 (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 | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | OK | ERROR | ||||||||||
|
To the developers/maintainers of the miRspongeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRspongeR.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: miRspongeR |
| Version: 2.13.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL miRspongeR |
| StartedAt: 2025-06-18 16:00:03 -0400 (Wed, 18 Jun 2025) |
| EndedAt: 2025-06-18 16:01:10 -0400 (Wed, 18 Jun 2025) |
| EllapsedTime: 67.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL miRspongeR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘miRspongeR’ ...
** this is package ‘miRspongeR’ version ‘2.13.2’
** 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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -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 miRspongeR.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-miRspongeR/00new/miRspongeR/libs
** R
** 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 (miRspongeR)