[Rcpp-devel] Possible regression in R-3.2.3 or Rcpp 0.12.3

Paul Johnson pauljohn32 at gmail.com
Thu Jan 28 20:19:18 CET 2016


Could I ask for some fresh eyes on this problem?

I need to diagnose a segmentation fault that started appearing this
week after we updated to R-3.2.3 and also Rcpp updated to 0.12.3 at
same time.

> library(openxlsx)
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] openxlsx_3.0.0

loaded via a namespace (and not attached):
[1] Rcpp_0.11.3
> dat <- read.xlsx("Failure_to_Import.xlsx", colNames = TRUE)

 *** caught segfault ***
address 0x35117000, cause 'memory not mapped'

 1: .Call("openxlsx_readWorkbook", v, r, string_refs, isDate, nRows,
  colNames, skipEmptyRows, origin, clean_names, PACKAGE = "openxlsx")
 2: read.xlsx.default("Failure_to_Import.xlsx", colNames = TRUE)
 3: read.xlsx("Failure_to_Import.xlsx", colNames = TRUE)
aborting ...

I have a fullly reproducible example:


This failure surfaced on the Centos 7 linux systems yesterday, but I
did not see it in Ubuntu until I updated Rcpp to version 0.12.3.  We
were comparing versions, that was the only difference I could see.
But then I removed Rcpp and installed from source 0.12.2 but the error
now happens with Rcpp 0.12.2.

I have got too many balls in the air to know where to start on this one.

One thing I wonder if it is necessary to completely erase and
reinstall all packages that depend on Rcpp in order to get a clean run
at this.

I thought the issue was Centos updates and possibly a funny GCC setup
there, but now same problem is happening in Ubuntu.

We've written to the openxlsx author to see if he has ideas,  but I
note that his package did not update during this process.

I am going to see about downgrading R to previous version, see if
problem disappears.


Paul E. Johnson
Professor, Political Science        Director
1541 Lilac Lane, Room 504      Center for Research Methods
University of Kansas                 University of Kansas
http://pj.freefaculty.org              http://crmda.ku.edu

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