New version crashes R

[waynelapierre]

The recent updated RPostgres crashes R when running a code that used to work (account information is not disclosed):

require(RPostgres)
wrds <- dbConnect(drv = Postgres(), 
                  host = "wrds-pgdata.wharton.upenn.edu",
                  port = 9737,
                  user = "username", 
                  password = "password", 
                  sslmode = "require",
                  dbname = "wrds")

My session information is as follows:

R version 4.0.5 (2021-03-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 34 (Workstation Edition)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libflexiblas.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] RPostgres_1.4.0

loaded via a namespace (and not attached):
 [1] bit_4.0.4       compiler_4.0.5  ellipsis_0.3.2  hms_1.1.0      
 [5] DBI_1.1.1       tools_4.0.5     rstudioapi_0.13 Rcpp_1.0.7     
 [9] bit64_4.0.5     vctrs_0.3.8     blob_1.2.2      lifecycle_1.0.1
[13] pkgconfig_2.0.3 rlang_0.4.11   

I reverted to version 1.3.3 and it works again.

[krlmlr]

Thanks for the report, sorry for the trouble.

Can you try running from a shell, is there an output before the crash? Can you compile RPostgres from source to do a git bisect to understand what causes the crash?

[krlmlr]

What does RPostgres:::client_version() show?

[waynelapierre]

RPostgres:::client_version() generates 130004 for both 1.3.3 and 1.4.0.
When I run the code (in my thread above) with 1.4.0 in shell, I got this error message:

/usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = const char*; _Alloc = std::allocator<const char*>; std::vector<_Tp, _Alloc>::reference = const char*&; std::vector<_Tp, _Alloc>::size_type = long unsigned int]: Assertion '__n < this->size()' failed.
Aborted (core dumped)

[krlmlr]

Thanks, that helps.

Can you compile RPostgres from source to do a git bisect to understand what causes the crash? Rough instructions:

git clone https://github.com/r-dbi/RPostgres.git
cd RPostgres
git bisect bad v1.4.0
git bisect good v1.3.3
cp ... test.R
git bisect run R -q -f test.R

with test.R containing:

system("git clean -fdx")
pkgload::load_all()
dbConnect(...)

The process might run for ~1 hour, much faster if ccache is active.

Let me know if you need more info.

[krlmlr]

Looking at the changes to the C++ code since v1.3.3, I think I might have found the problem.

[krlmlr]

The first PR might fix the cause, the second PR the symptoms (but crash at the first query).

Can you please install with

remotes::install_github("r-dbi/RPostgres#345")

and test?

[waynelapierre]

Problem solved. Thank God that I don't have to do the one-hour git bisect. Thank you for this great package and quick reply.

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