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This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4358
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 1287/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoClone2 1.12.0  (landing page)
Benjamin Story
Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025)
git_url: https://git.bioconductor.org/packages/mitoClone2
git_branch: RELEASE_3_20
git_last_commit: b33a8ad
git_last_commit_date: 2024-10-29 11:02:30 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

INSTALL results for mitoClone2 on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: mitoClone2
Version: 1.12.0
Command: /home/biocbuild/R/R/bin/R CMD INSTALL mitoClone2
StartedAt: 2025-01-08 20:21:24 -0000 (Wed, 08 Jan 2025)
EndedAt: 2025-01-08 20:22:20 -0000 (Wed, 08 Jan 2025)
EllapsedTime: 56.5 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL mitoClone2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘mitoClone2’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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 "/home/biocbuild/R/R-4.4.2/site-library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "/home/biocbuild/R/R-4.4.2/site-library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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;
      |         ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o mitoClone2.so bam2R_10x.o /home/biocbuild/R/R-4.4.2/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.4.2/site-library/00LOCK-mitoClone2/00new/mitoClone2/libs
** 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
** 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 (mitoClone2)