Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-12-23 11:42 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1280/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoClone2 1.13.0  (landing page)
Benjamin Story
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/mitoClone2
git_branch: devel
git_last_commit: 020fb39
git_last_commit_date: 2024-10-29 11:02:30 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'deepSNV' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'deepSNV' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


BUILD BIN results for mitoClone2 on palomino7

To the developers/maintainers of the mitoClone2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mitoClone2.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: mitoClone2
Version: 1.13.0
Command: rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=mitoClone2.buildbin-libdir mitoClone2_1.13.0.tar.gz
StartedAt: 2024-12-23 07:18:47 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 07:20:21 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 94.6 seconds
RetCode: 0
Status:   OK  
PackageFile: mitoClone2_1.13.0.zip
PackageFileSize: 6.728 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=mitoClone2.buildbin-libdir mitoClone2_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'mitoClone2' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
../inst/SCITEpkg/findBestTrees.cpp:58:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch]
   58 | double gamma = 1;
      |        ^~~~~
mkdir -p "E:/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "E:/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment]
    6 |  /**************************************************************************************
      |   
bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment]
    8 | /**********************************************************************
      |  
bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
bam2R_10x.cpp:75:17: warning: unused variable 'bc_absent' [-Wunused-variable]
   75 |             int bc_absent;
      |                 ^~~~~~~~~
bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable]
  158 |     hts_itr_t *iter = NULL;
      |                ^~~~
bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable]
  161 |     int c = 0;
      |         ^
g++ -std=gnu++17 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* MD5 sums
packaged installation of 'mitoClone2' as mitoClone2_1.13.0.zip
* DONE (mitoClone2)