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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FitHiC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings FitHiC_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/FitHiC.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FitHiC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FitHiC’ version ‘1.25.0’
* 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 ‘FitHiC’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is 28.1Mb
  sub-directories of 1Mb or more:
    extdata  26.7Mb
    libs      1.3Mb
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘FitHiC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FitHiC
> ### Title: Fit-Hi-C
> ### Aliases: FitHiC
> 
> ### ** Examples
> 
> fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_EcoRI.gz",
+     package = "FitHiC")
> intersfile <- system.file("extdata", "contactCounts/Duan_yeast_EcoRI.gz",
+     package = "FitHiC")
> outdir <- file.path(getwd(), "Duan_yeast_EcoRI")
> FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_EcoRI",
+     distUpThres=250000, distLowThres=10000)
Fit-Hi-C is processing ...
Running parse_Fragsfile method ...
Complete parse_Fragsfile method [OK]
Running parse_Intersfile method ...
Complete parse_Intersfile method [OK]
Running generate_FragPairs method ...
Complete generate_FragPairs method [OK]
Running read_All_Interactions method ...
Complete read_All_Interactions method [OK]
Running calculating_Probabilities method ...
Writing Duan_yeast_EcoRI.fithic_pass1.txt
Complete calculating_Probabilities method [OK]
Running fit_Spline method ...
Writing p-values to file Duan_yeast_EcoRI.spline_pass1.significances.txt.gz
Complete fit_Spline method [OK]
Running calculating_Probabilities method ...
Writing Duan_yeast_EcoRI.fithic_pass2.txt
Complete calculating_Probabilities method [OK]
Running fit_Spline method ...
Writing p-values to file Duan_yeast_EcoRI.spline_pass2.significances.txt.gz
Complete fit_Spline method [OK]
Execution of Fit-Hi-C completed successfully. [DONE]
.Primitive("return")
> 
> fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_HindIII.gz",
+     package = "FitHiC")
> intersfile <- system.file("extdata", "contactCounts/Duan_yeast_HindIII.gz",
+     package = "FitHiC")
> outdir <- file.path(getwd(), "Duan_yeast_HindIII")
> FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_HindIII",
+     distUpThres=250000, distLowThres=10000)
Fit-Hi-C is processing ...
Running parse_Fragsfile method ...
Complete parse_Fragsfile method [OK]
Running parse_Intersfile method ...
Complete parse_Intersfile method [OK]
Running generate_FragPairs method ...
Complete generate_FragPairs method [OK]
Running read_All_Interactions method ...
Complete read_All_Interactions method [OK]
Running calculating_Probabilities method ...
Writing Duan_yeast_HindIII.fithic_pass1.txt
Complete calculating_Probabilities method [OK]
Running fit_Spline method ...
Writing p-values to file Duan_yeast_HindIII.spline_pass1.significances.txt.gz
Complete fit_Spline method [OK]
Running calculating_Probabilities method ...
Writing Duan_yeast_HindIII.fithic_pass2.txt
Complete calculating_Probabilities method [OK]
Running fit_Spline method ...
Writing p-values to file Duan_yeast_HindIII.spline_pass2.significances.txt.gz
Complete fit_Spline method [OK]
Execution of Fit-Hi-C completed successfully. [DONE]
.Primitive("return")
> 
> fragsfile <- system.file("extdata",
+     "fragmentLists/Dixon_hESC_HindIII_hg18_combineFrags10_chr1.gz",
+     package = "FitHiC")
> intersfile <- system.file("extdata",
+     "contactCounts/Dixon_hESC_HindIII_hg18_combineFrags10_chr1.gz",
+     package = "FitHiC")
> outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_combineFrags10_chr1")
> FitHiC(fragsfile, intersfile, outdir,
+     libname="Dixon_hESC_HindIII_hg18_combineFrags10_chr1", noOfBins=200,
+     distUpThres=5000000, distLowThres=50000)
Fit-Hi-C is processing ...
Running parse_Fragsfile method ...
Complete parse_Fragsfile method [OK]
Running parse_Intersfile method ...
Complete parse_Intersfile method [OK]
Running generate_FragPairs method ...
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘fithic.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/FitHiC.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FitHiC
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘FitHiC’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitHiC_init.c -o FitHiC_init.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c helper.cpp -o helper.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o FitHiC.so FitHiC_init.o RcppExports.o helper.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-FitHiC/00new/FitHiC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (FitHiC)