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This page was generated on 2022-04-13 12:05:37 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for mitoClone2 on nebbiolo2


To the developers/maintainers of the mitoClone2 package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1177/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoClone2 1.0.0  (landing page)
Benjamin Story
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/mitoClone2
git_branch: RELEASE_3_14
git_last_commit: 2b6203f
git_last_commit_date: 2021-10-26 13:11:28 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mitoClone2
Version: 1.0.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:mitoClone2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings mitoClone2_1.0.0.tar.gz
StartedAt: 2022-04-12 08:17:06 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:22:19 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 313.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: mitoClone2.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:mitoClone2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings mitoClone2_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/mitoClone2.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitoClone2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mitoClone2’ version ‘1.0.0’
* 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 ... WARNING
Found the following significant warnings:
  ../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
See ‘/home/biocbuild/bbs-3.14-bioc/meat/mitoClone2.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 R 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.14-bioc/R/library/mitoClone2/libs/mitoClone2.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (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. 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 53.355  0.073   53.43
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/mitoClone2.Rcheck/00check.log’
for details.



Installation output

mitoClone2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL mitoClone2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘mitoClone2’ ...
** using staged installation
** libs
g++ -std=gnu++14 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
../inst/SCITEpkg/findBestTrees.cpp:56:8: warning: built-in function ‘gamma’ declared as non-function [-Wbuiltin-declaration-mismatch]
   56 | double gamma = 1;
      |        ^~~~~
../inst/SCITEpkg/mcmcBinTreeMove.cpp: In function ‘int pickNodeToMove(int*, int)’:
../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
   75 | }
      | ^
mkdir -p "/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/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:75:10: 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++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o mitoClone2.so bam2R_10x.o /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 
 13.440   1.010  14.431 

Example timings

mitoClone2.Rcheck/mitoClone2-Ex.timings

nameusersystemelapsed
bam2R_10x0.3120.0310.346
baseCountsFromBamList0.1620.0000.162
clusterMetaclones0.0430.0000.043
getAlleleCount0.0060.0000.007
getCloneLikelihood0.0050.0000.005
getVarsCandidate0.0050.0000.005
mitoPlot0.7980.0120.809
mut2GR0.1920.0400.231
mutationCallsFromCohort1.0260.0601.085
mutationCallsFromExclusionlist2.8090.1122.921
mutationCallsFromMatrix1.1810.0001.181
overwriteMetaclones0.0140.0000.015
plotClones0.2420.0080.250
pullcountsVars1.1880.0041.193
quick_cluster0.10.00.1
removeWindow0.480.000.48
setVarsCandidate0.0050.0000.005
varCluster53.355 0.07353.430