[Debian-med-packaging] Bug#860876: Bug#860876: reapr: FTBFS: Error in system call: R CMD BATCH 00.Sample/gc_vs_cov.R 00.Sample/gc_vs_cov.Rout

[Sascha Steinbiss]

reassign 860876 r-cran-kernsmooth
thanks


Hi Chris,

thanks for your bug report. I can reproduce the problem; it looks like an R component within REAPR’s build time tests has started to fail, causing the whole build to break.

[…]
>  [REAPR preprocess] Error in system call:
>  R CMD BATCH 00.Sample/gc_vs_cov.R 00.Sample/gc_vs_cov.Rout
>  debian/rules:33: recipe for target 'override_dh_auto_test' failed
>  make[1]: *** [override_dh_auto_test] Error 1
>  make[1]: Leaving directory '«BUILDDIR»'
>  debian/rules:4: recipe for target 'build' failed
>  make: *** [build] Error 2
>  dpkg-buildpackage: error: debian/rules build gave error exit status 2

I have traced the error down to the R script in question used by the tests (00.Sample/gc_vs_cov.R). Indeed there is an error running it, which is apparent when looking at 00.Sample/gc_vs_cov.Rout:

  […]
  > data=read.csv(file="00.Sample/gc_vs_cov.dat", colClasses=c("numeric", "integer"), header=F, sep="	", comment.char="")
  > l=lowess(data)
  > data_out=unique(data.frame(l$x,l$y))
  > write(t(data_out), sep="	", ncolumns=2, file="00.Sample/gc_vs_cov.lowess.dat.tmp")
  > pdf("00.Sample/gc_vs_cov.lowess.pdf")
  >   smoothScatter(data, xlab="GC", ylab="Coverage")
  Error in linbin2D(x, gpoints1, gpoints2) : object 'F_lbtwod' not found
  Calls: smoothScatter -> <Anonymous> -> <Anonymous> -> linbin2D
  Execution halted

It looks like r-cran-kernsmooth has trouble finding the Fortran components on newer R versions (I tested 3.4.0 from unstable). It works fine on R 3.3.3 (as it is in stretch). To reproduce without messing with REAPR, it should even be enough to try and run the tests/bkfe.R script included in the kernsmooth source:

  [vagrant at vagrant-debian:/vagrant/kernsmooth-2.23-15/tests] $ R CMD BATCH bkfe.R
  [vagrant at vagrant-debian:/vagrant/kernsmooth-2.23-15/tests] $ cat bkfe.Rout
  R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
  Copyright (C) 2017 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.

  > ## failed in bkfe with exaxt powers of 2 prior to 2.23-5
  > library(KernSmooth)
  KernSmooth 2.23 loaded
  Copyright M. P. Wand 1997-2009
  > x <- 1:100
  > dpik(x, gridsize = 256)
  Error in linbin(x, gpoints, truncate) : object 'F_linbin' not found
  Calls: dpik -> linbin
  Execution halted

This also works with no problems when run using R 3.3.3. Unfortunately, I am not an R expert, so could someone with some more experience please have a look? Thanks!

Cheers
Sascha

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