Hello
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)
locale:
[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
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=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'
Traceback:
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:
http://pj.freefaculty.org/scraps/openxlsx_failure.zip
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.
pj
--
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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