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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 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" 4373
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: 2024-12-23 13:40 -0500 (Mon, 23 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  


INSTALL results for mitoClone2 on nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL mitoClone2
StartedAt: 2024-12-23 15:20:29 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 15:21:17 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 47.6 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL mitoClone2
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘mitoClone2’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 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 "/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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:21: warning: "R_NO_REMAP" redefined
   21 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
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 -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o mitoClone2.so bam2R_10x.o /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/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)