rchk error

[NicChr]

Hi, I'm getting an rchk error and not sure if it relates to my code directly or something I can't fix on my side.
https://raw.githubusercontent.com/kalibera/cran-checks/master/rchk/results/fastplyr.out

Many thanks!

The error:

Function cpp11::writable::r_vector<SEXPREC*>::reserve_data(SEXPREC*, bool, long)
  [UP] calling allocating function cpp11::writable::r_vector<SEXPREC*>::resize_names(SEXPREC*, long) with a fresh pointer (names <arg 1>) cpp11/include/cpp11/r_vector.hpp:1329

[DavisVaughan]

We've also seen this in one other package so I'll see what I can do
r-lib/archive@d1fca9d#diff-d0bd7e3af6adbdcc064b3bc426e211cc595cbe2c9627d2cf5f66a505c63c4ea7R1330-R1332

Nothing for you to do on your end, but thanks for reporting!

[pepijn-devries]

Hi there,

Has it been confirmed that this commit fixed the issue reported here? This commit is included in the latest release (0.5.1) which is also on CRAN. However, I'm still receiving similar rchk reports as reported here. See for instance:

https://raw.githubusercontent.com/kalibera/cran-checks/master/rchk/results/ProTrackR2.out
https://raw.githubusercontent.com/kalibera/cran-checks/master/rchk/results/adfExplorer.out

Are these issues indeed related? Should this have been fixed by #409? Or is this something I need to fix myself?

[jayhesselberth]

#409 doesn't appear to have fixed the rchk issue, still being flagged in several packages:

https://cloud.r-project.org/web/checks/check_results_cpp11bigwig.html
https://cran.r-project.org/web/checks/check_results_tweenr.html

[jayhesselberth]

I wonder if it should be something like:

if (Rf_xlength(names) != size) {
  SEXP resized_names = PROTECT(resize_names(names, size));
  Rf_setAttrib(out, R_NamesSymbol, resized_names);
  UNPROTECT(1);
}

[jwood000]

I too am getting rchk issues:

https://raw.githubusercontent.com/kalibera/cran-checks/master/rchk/results/RcppAlgos.out

I haven't submitted an update to my package yet, but I suspect they won't accept an update until this has been addressed.

I have addressed the rchk issue in my package (the 'Suspicious Call').

Thanks

[pepijn-devries]

@r-lib @DavisVaughan It looks like this issue needs to be reopened?

[jwood000]

I think the error message from rchk is pretty telling:

Function ... reserve_data ... calling allocating function ... resize_names

If we look at the current definition of reserve_data found here:

cpp11/inst/include/cpp11/r_vector.hpp

Line 1321 in 2938879

inline SEXP r_vector<T>::reserve_data(SEXP x, bool is_altrep, R_xlen_t size) {

We see the following code:

.
.
.
  // Resize names, if required
  // Protection seems needed to make rchk happy
  SEXP names = PROTECT(Rf_getAttrib(x, R_NamesSymbol));
  if (names != R_NilValue) {
    if (Rf_xlength(names) != size) {
      names = resize_names(names, size);
    }
    Rf_setAttrib(out, R_NamesSymbol, names);
  }
.
.
.

The problem line is names = resize_names(names, size);. We can rewrite the above as:

.
.
.
  // Resize names, if required
  // Protection seems needed to make rchk happy
  SEXP names = PROTECT(Rf_getAttrib(x, R_NamesSymbol));
  if (names != R_NilValue) {
    if (Rf_xlength(names) != size) {
      SEXP names_resized = PROTECT(resize_names(names, size));
      Rf_setAttrib(out, R_NamesSymbol, names_resized);
      UNPROTECT(1);
    } else {
      Rf_setAttrib(out, R_NamesSymbol, names);
    }
  }
.
.
.

[DavisVaughan]

From what I can tell, every listed package did the rchk run on 2024-11-21

The cpp11 release was on 2024-12-04

The full message is

Function cpp11::writable::r_vector<SEXPREC*>::reserve_data(SEXPREC*, bool, long)
  [UP] calling allocating function cpp11::writable::r_vector<SEXPREC*>::resize_names(SEXPREC*, long) with a fresh pointer (names <arg 1>) cpp11/include/cpp11/r_vector.hpp:1329

The main problem being

with a fresh pointer (names <arg 1>)

Which is why the fix protects names.
https://github.com/r-lib/cpp11/pull/409/files

If anyone can reproduce with CRAN cpp11 and provide an easy way for me to reproduce as well, then we can reopen. But I think CRAN just hasn't rerun rchk on these packages.

[DavisVaughan]

An exception is cpp11bigwig, run on 2025-01-09
https://raw.githubusercontent.com/kalibera/cran-checks/master/rchk/results/cpp11bigwig.out

Function cpp11::writable::r_vector<SEXPREC*>::r_vector(std::initializer_list<cpp11::named_arg>)::{lambda()#1}::operator()() const
  [UP] unprotected variable names while calling allocating function Rf_mkCharCE cpp11/include/cpp11/list.hpp:91

That is a different issue from the one I tried to fix. I will open a different issue for that.

[pepijn-devries]

An exception is cpp11bigwig, run on 2025-01-09 https://raw.githubusercontent.com/kalibera/cran-checks/master/rchk/results/cpp11bigwig.out

Function cpp11::writable::r_vector<SEXPREC*>::r_vector(std::initializer_list<cpp11::named_arg>)::{lambda()#1}::operator()() const
  [UP] unprotected variable names while calling allocating function Rf_mkCharCE cpp11/include/cpp11/list.hpp:91

That is a different issue from the one I tried to fix. I will open a different issue for that.

This test result is from January:

https://raw.githubusercontent.com/kalibera/cran-checks/master/rchk/results/adfExplorer.out

[DavisVaughan]

Yes, and that is a different issue from the original one here. I opened #445 for this.