Junpeng Zhang
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/miRspongeR |
| git_branch: devel |
| git_last_commit: 46a1461 |
| git_last_commit_date: 2025-06-18 23:30:12 -0400 (Wed, 18 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 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" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1298/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miRspongeR 2.13.4 (landing page) Junpeng Zhang
| nebbiolo2 | Linux (Ubuntu 24.04.3 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 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 2.13.4 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL miRspongeR |
| StartedAt: 2025-08-14 16:54:18 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-14 16:55:36 -0400 (Thu, 14 Aug 2025) |
| EllapsedTime: 77.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL miRspongeR
###
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'miRspongeR' ...
** this is package 'miRspongeR' version '2.13.4'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
Error in loadNamespace(x) : there is no package called 'zlibbioc'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -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;
| ^~~
OCG_algorithm.c:475:5: warning: '*Cl' may be used uninitialized [-Wmaybe-uninitialized]
475 | Cl[0][0]=1;
| ~~^~~
Error in loadNamespace(x) : there is no package called 'zlibbioc'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c complex.c -o complex.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c edge_duplicates.cpp -o edge_duplicates.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linkcomm_edgesims.cpp -o linkcomm_edgesims.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linkcomm_edgesims_all.cpp -o linkcomm_edgesims_all.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linkcomm_functions.cpp -o linkcomm_functions.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linkcomm_hclust.cpp -o linkcomm_hclust.o
Error in loadNamespace(x) : there is no package called 'zlibbioc'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c linkcomm_init.c -o linkcomm_init.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linkcomm_linkdensities.cpp -o linkcomm_linkdensities.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linkcommhclust_order.cpp -o linkcommhclust_order.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_OCG.cpp -o read_OCG.o
Error in loadNamespace(x) : there is no package called 'zlibbioc'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o
/bin/sh: -c: line 1: unexpected EOF while looking for matching `"'
/bin/sh: -c: line 1: unexpected EOF while looking for matching `"'
/bin/sh: -c: line 1: unexpected EOF while looking for matching `"'
/bin/sh: -c: line 1: unexpected EOF while looking for matching `"'
g++ -std=gnu++17 -shared -s -static-libgcc -o miRspongeR.dll tmp.def 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 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-miRspongeR/00new/miRspongeR/libs/x64
** 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'
** 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)