R devel - Jan 2023 - Sys.getenv(): Error in substring(x, m + 1L) : invalid multibyte string at '<ff>' if an environment variable contains \xFF

On 1/30/23 23:01, Henrik Bengtsson wrote:
> /Hello.
>
> SUMMARY:
> $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e
"Sys.getenv()"
> Error in substring(x, m + 1L) : invalid multibyte string at
'<ff>'
>
> $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e
"Sys.getenv('BOOM')"
> [1] "\xff"
>
> BACKGROUND:
> I launch R through an Son of Grid Engine (SGE) scheduler, where the R
> process is launched on a compute host via  'qrsh', which part of
SGE.
> Without going into details, 'mpirun' is also involved. Regardless,
in
> this process, an 'qrsh'-specific environment variable
'QRSH_COMMAND'
> is set automatically.  The value of this variable comprise of a string
> with \xff (ASCII 255) injected between the words.  This is by design
> of SGE [1].  Here is an example of what this environment variable may
> look like:
>
> QRSH_COMMAND=
orted\xff--hnp-topo-sig\xff2N:2S:32L3:128L2:128L1:128C:256H:x86_64\xff-mca\xffess\xff\"env\"\xff-mca\xfforte_ess_jobid\xff\"3473342464\"\xff-mca\xfforte_ess_vpid\xff1\xff-mca\xfforte_ess_num_procs\xff\"3\"\xff-mca\xfforte_hnp_uri\xff\"3473342464.0;tcp://192.168.1.13:50847\"\xff-mca\xffplm\xff\"rsh\"\xff-mca\xfforte_tag_output\xff\"1\"\xff--tree-spawn"
>
> where each \xff is a single byte 255=0xFF=\xFF.
>
>
> ISSUE:
> An environment variable with embedded 0xFF bytes in its value causes
> calls to Sys.getenv() to produce an error when running R in a UTF-8
> locale. Here is a minimal example on Linux:
>
> $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e
"Sys.getenv()"
> Error in substring(x, m + 1L) : invalid multibyte string at
'<ff>'
> Calls: Sys.getenv -> substring
> In addition: Warning message:
> In regexpr("=", x, fixed = TRUE) :
>    input string 134 is invalid in this locale
> Execution halted
>
>
> WORKAROUND:
> The workaround is to (1) identify any environment variables with
> invalid UTF-8 symbols, and (2) prune or unset those variables before
> launching R, e.g. in my SGE case, launching R using:
>
> QRSH_COMMAND= Rscript --vanilla -e "Sys.getenv()"
>
> avoid the problem.  Having to unset/modify environment variables
> because R doesn't like them, see a bit of an ad-hoc hack to me.  Also,
> if you are not aware of this problem, or not a savvy R user, it can be
> quite tricky to track down the above error message, especially if
> Sys.getenv() is called deep down in some package dependency.
>
>
> DISCUSSION/SUGGESTION/ASK:
> My suggestion would be to make Sys.getenv() robust against any type of
> byte values in environment variable strings.
>
> The error occurs in Sys.getenv() from:
>
>          x <- .Internal(Sys.getenv(character(), ""))
>          m <- regexpr("=", x, fixed = TRUE)  ## produces a
warning
>          n <- substring(x, 1L, m - 1L)
>          v <- substring(x, m + 1L)  ## produces the error
>
> I know too little about string encodings, so I'm not sure what the
> best approach would be here, but maybe falling back to parsing strings
> that are invalid in the current locale using the C locale would be
> reasonable?  Maybe Sys.getenv() should always use the C locale for
> this. It looks like Sys.getenv(name) does this, e.g.
>
> $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e
"Sys.getenv('BOOM')"
> [1] "\xff"
>
> I'd appreciate any comments and suggestions. I'm happy to file a
bug
> report on BugZilla, if this is a bug.
This discussion comes from Python: https://bugs.python.org/issue4006
(it says Python skips such environment variables)

The problem of invalid strings in environment variables is a similar to 
the problem of invalid strings in file names. Both variables and file 
names are something people want to use as strings in programs, scripts, 
texts, but at the same time these may in theory not be valid strings. 
Working with (potentially) invalid strings (almost) transparently is 
much harder than with valid strings; even if R decided to do that, it 
would be hard to implement and take long and only work for some 
operations, most will still throw errors. In addition, in practice 
invalid strings are almost always due to an error, particularly so in 
file names or environment variables. Such errors are often worth 
catching (wrong encoding declaration, etc), even though perhaps not always.

In practice, this instance can only be properly fixed at the source, [1] 
should not do this. split_command() will run into problems with 
different software, not just R.

There should be a way to split the commands in ASCII (using some sort of 
quoting/escaping). Using \xFF is flawed also simply because it may be 
present in the commands, if we followed the same logic of that every 
byte is fine. So the code is buggy even regardless of multi-byte encodings.

Re difficulty to debug, I think the error message is clear and if 
packages catch and hide errors, that'd be bad design of such packages, R 
couldn't really do much about that. This needs to be fixed at [1].

Tomas
>
> Henrik
>
> [1]
https://github.com/gridengine/gridengine/blob/master/source/clients/qrsh/qrsh_starter.c#L462-L466
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Tomas,

I think you're not addressing the actual issue which is a clear regression
in Sys.getenv() [because it used to work and still works for single env var, but
not a list] and the cryptic error due to that regression (caused by changes in
R-devel). So in either case, Sys.getenv needs fixing (i.e., this should really
go to the bugzilla). Its behavior is currently inconsistent.

The quoted Python discussion diverges very quickly into file name discussions,
but I think that is not relevant here - environment variables are essentially
data "blobs" that have application-specific meaning. They just chose
to drop them because they didn't want to make a decision.

I don't have a strong opinion on this, but Sys.getenv("FOO") and
Sys.getenv()[["FOO"]] should not yield two different results. I would
argue that if we want to make specific checks, we should make them conditional -
even if the default is to add them. Again, the error is due to the
implementation of Sys.getenv() breaking in R-devel, not due to any design
decision.

Cheers,
Simon

> On Jan 31, 2023, at 1:04 PM, Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
> 
> 
> On 1/30/23 23:01, Henrik Bengtsson wrote:
>> /Hello.
>> 
>> SUMMARY:
>> $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e
"Sys.getenv()"
>> Error in substring(x, m + 1L) : invalid multibyte string at
'<ff>'
>> 
>> $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e
"Sys.getenv('BOOM')"
>> [1] "\xff"
>> 
>> BACKGROUND:
>> I launch R through an Son of Grid Engine (SGE) scheduler, where the R
>> process is launched on a compute host via  'qrsh', which part
of SGE.
>> Without going into details, 'mpirun' is also involved.
Regardless, in
>> this process, an 'qrsh'-specific environment variable
'QRSH_COMMAND'
>> is set automatically.  The value of this variable comprise of a string
>> with \xff (ASCII 255) injected between the words.  This is by design
>> of SGE [1].  Here is an example of what this environment variable may
>> look like:
>> 
>> QRSH_COMMAND=
orted\xff--hnp-topo-sig\xff2N:2S:32L3:128L2:128L1:128C:256H:x86_64\xff-mca\xffess\xff\"env\"\xff-mca\xfforte_ess_jobid\xff\"3473342464\"\xff-mca\xfforte_ess_vpid\xff1\xff-mca\xfforte_ess_num_procs\xff\"3\"\xff-mca\xfforte_hnp_uri\xff\"3473342464.0;tcp://192.168.1.13:50847\"\xff-mca\xffplm\xff\"rsh\"\xff-mca\xfforte_tag_output\xff\"1\"\xff--tree-spawn"
>> 
>> where each \xff is a single byte 255=0xFF=\xFF.
>> 
>> 
>> ISSUE:
>> An environment variable with embedded 0xFF bytes in its value causes
>> calls to Sys.getenv() to produce an error when running R in a UTF-8
>> locale. Here is a minimal example on Linux:
>> 
>> $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e
"Sys.getenv()"
>> Error in substring(x, m + 1L) : invalid multibyte string at
'<ff>'
>> Calls: Sys.getenv -> substring
>> In addition: Warning message:
>> In regexpr("=", x, fixed = TRUE) :
>>   input string 134 is invalid in this locale
>> Execution halted
>> 
>> 
>> WORKAROUND:
>> The workaround is to (1) identify any environment variables with
>> invalid UTF-8 symbols, and (2) prune or unset those variables before
>> launching R, e.g. in my SGE case, launching R using:
>> 
>> QRSH_COMMAND= Rscript --vanilla -e "Sys.getenv()"
>> 
>> avoid the problem.  Having to unset/modify environment variables
>> because R doesn't like them, see a bit of an ad-hoc hack to me. 
Also,
>> if you are not aware of this problem, or not a savvy R user, it can be
>> quite tricky to track down the above error message, especially if
>> Sys.getenv() is called deep down in some package dependency.
>> 
>> 
>> DISCUSSION/SUGGESTION/ASK:
>> My suggestion would be to make Sys.getenv() robust against any type of
>> byte values in environment variable strings.
>> 
>> The error occurs in Sys.getenv() from:
>> 
>>         x <- .Internal(Sys.getenv(character(), ""))
>>         m <- regexpr("=", x, fixed = TRUE)  ## produces a
warning
>>         n <- substring(x, 1L, m - 1L)
>>         v <- substring(x, m + 1L)  ## produces the error
>> 
>> I know too little about string encodings, so I'm not sure what the
>> best approach would be here, but maybe falling back to parsing strings
>> that are invalid in the current locale using the C locale would be
>> reasonable?  Maybe Sys.getenv() should always use the C locale for
>> this. It looks like Sys.getenv(name) does this, e.g.
>> 
>> $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e
"Sys.getenv('BOOM')"
>> [1] "\xff"
>> 
>> I'd appreciate any comments and suggestions. I'm happy to file
a bug
>> report on BugZilla, if this is a bug.
> This discussion comes from Python: https://bugs.python.org/issue4006
> (it says Python skips such environment variables)
> 
> The problem of invalid strings in environment variables is a similar to the
problem of invalid strings in file names. Both variables and file names are
something people want to use as strings in programs, scripts, texts, but at the
same time these may in theory not be valid strings. Working with (potentially)
invalid strings (almost) transparently is much harder than with valid strings;
even if R decided to do that, it would be hard to implement and take long and
only work for some operations, most will still throw errors. In addition, in
practice invalid strings are almost always due to an error, particularly so in
file names or environment variables. Such errors are often worth catching (wrong
encoding declaration, etc), even though perhaps not always.
> 
> In practice, this instance can only be properly fixed at the source, [1]
should not do this. split_command() will run into problems with different
software, not just R.
> 
> There should be a way to split the commands in ASCII (using some sort of
quoting/escaping). Using \xFF is flawed also simply because it may be present in
the commands, if we followed the same logic of that every byte is fine. So the
code is buggy even regardless of multi-byte encodings.
> 
> Re difficulty to debug, I think the error message is clear and if packages
catch and hide errors, that'd be bad design of such packages, R couldn't
really do much about that. This needs to be fixed at [1].
> 
> Tomas
> 
>> 
>> Henrik
>> 
>> [1]
https://github.com/gridengine/gridengine/blob/master/source/clients/qrsh/qrsh_starter.c#L462-L466
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>