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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 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 1287/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoClone2 1.12.0  (landing page)
Benjamin Story
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows 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  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for mitoClone2 on kunpeng2

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 check --install=check:mitoClone2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mitoClone2_1.12.0.tar.gz
StartedAt: 2024-11-20 09:59:14 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:06:53 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 459.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: mitoClone2.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:mitoClone2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mitoClone2_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mitoClone2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitoClone2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mitoClone2’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mitoClone2’ can be installed ... OK
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
mitoPlot: no visible binding for global variable ‘gene’
Undefined global functions or variables:
  gene
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'mitoPlot.Rd':
mitoPlot
  Code: function(variants, patient = NULL, genome = "hg38",
                 customGenome = NULL, showLegend = TRUE, showLabel =
                 TRUE)
  Docs: function(variants, patient = NULL, genome = "hg38", showLegend
                 = TRUE, showLabel = TRUE)
  Argument names in code not in docs:
    customGenome
  Mismatches in argument names:
    Position: 4 Code: customGenome Docs: showLegend
    Position: 5 Code: showLegend Docs: showLabel

Codoc mismatches from Rd file 'mutationCallsFromCohort.Rd':
mutationCallsFromCohort
  Code: function(BaseCounts, sites, patient, MINREADS = 5, MINCELL =
                 20, MINFRAC = 0.1, MINCELLS.PATIENT = 10,
                 MINFRAC.PATIENT = 0.01, MINFRAC.OTHER = 0.1,
                 USE.REFERENCE = TRUE, genome = "hg38", customGenome =
                 NULL)
  Docs: function(BaseCounts, sites, patient, MINREADS = 5, MINCELL =
                 20, MINFRAC = 0.1, MINCELLS.PATIENT = 10,
                 MINFRAC.PATIENT = 0.01, MINFRAC.OTHER = 0.1,
                 USE.REFERENCE = TRUE, genome = "hg38")
  Argument names in code not in docs:
    customGenome

Codoc mismatches from Rd file 'mutationCallsFromExclusionlist.Rd':
mutationCallsFromExclusionlist
  Code: function(BaseCounts, lim.cov = 20, min.af = 0.2,
                 min.num.samples = 0.01 * length(BaseCounts),
                 min.af.universal = min.af, universal.var.cells = 0.95
                 * length(BaseCounts), exclusionlists.use =
                 exclusionlists, max.var.na = 0.5, max.cell.na = 0.95,
                 genome = "hg38", customDNA = NULL, ncores = 1, ...)
  Docs: function(BaseCounts, lim.cov = 20, min.af = 0.2,
                 min.num.samples = 0.01 * length(BaseCounts),
                 min.af.universal = min.af, universal.var.cells = 0.95
                 * length(BaseCounts), exclusionlists.use =
                 exclusionlists, max.var.na = 0.5, max.cell.na = 0.95,
                 genome = "hg38", ncores = 1, ...)
  Argument names in code not in docs:
    customDNA
  Mismatches in argument names:
    Position: 11 Code: customDNA Docs: ncores
    Position: 12 Code: ncores Docs: ...

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4.1/site-library/mitoClone2/libs/mitoClone2.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
varCluster 77.412  0.155  77.707
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/mitoClone2.Rcheck/00check.log’
for details.


Installation output

mitoClone2.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘mitoClone2’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
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/R/R-4.4.1/site-library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "/home/biocbuild/R/R-4.4.1/site-library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -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 -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o mitoClone2.so bam2R_10x.o /home/biocbuild/R/R-4.4.1/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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)

Tests output

mitoClone2.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(mitoClone2)
> 
> test_check("mitoClone2")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 17.254   0.690  17.879 

Example timings

mitoClone2.Rcheck/mitoClone2-Ex.timings

nameusersystemelapsed
bam2R_10x0.6080.0270.640
baseCountsFromBamList0.2120.0000.215
clusterMetaclones0.0580.0000.059
getAlleleCount0.0070.0000.008
getCloneLikelihood0.0060.0000.006
getVarsCandidate0.0060.0000.006
mitoPlot0.9350.0520.988
mut2GR0.2030.0160.220
mutationCallsFromCohort1.4730.0481.572
mutationCallsFromExclusionlist2.6070.0752.689
mutationCallsFromMatrix1.6100.0161.630
overwriteMetaclones0.0160.0000.015
plotClones0.3410.0070.349
pullcountsVars1.4960.0111.511
quick_cluster0.1280.0040.133
removeWindow0.5160.0000.517
setVarsCandidate0.0060.0000.006
varCluster77.412 0.15577.707