On Jan 31, 2023, at 1:04 PM, Tomas Kalibera <tomas.kalib...@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
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