R devel - May 2017 - problem running test on a system without /etc/localtime

Hi all, 

A problem with tests while building R.

I'm packaging R for Sisyphus repository and package build environment,
by design, doesn't have /etc/localtime file present. This causes failure
with Sys.timeone during test run:

[builder at localhost tests]$ ../bin/R --vanilla < reg-tests-1d.R
> ## PR#17186 - Sys.timezone() on some Debian-derived platforms
> (S.t <- Sys.timezone())
Error in normalizePath("/etc/localtime") : 
  (converted from warning) path[1]="/etc/localtime": No such file or
  directory
  Calls: Sys.timezone -> normalizePath
  Execution halted

This is caused by this code:
> Sys.timezone
function (location = TRUE) 
{
    tz <- Sys.getenv("TZ", names = FALSE)
    if (!location || nzchar(tz)) 
        return(Sys.getenv("TZ", unset =
NA_character_))
>>  lt <- normalizePath("/etc/localtime")
[remainder of the code skkipped]

File /etc/loclatime is optional and is not guaranteed to be present on
any platform. And anyway, it is a good idea to first check that file 
exists before calling normalizePath. 

Sure, this can be worked around by setting TZ environment variable, but
that causes tests to fail in another place:

[builder at localhost tests]$ TZ="GMT" ../bin/R --vanilla <
reg-tests-1d.R
> ## format()ing invalid hand-constructed  POSIXlt  objects
> d <- as.POSIXlt("2016-12-06"); d$zone <- 1
> tools::assertError(format(d))
Error: Failed to get error in evaluating format(d)
Execution halted

It seems that the best solution will be to patch Sys.timezone.

-- 
KM

On 17 May 2017 at 03:35, Kirill Maslinsky wrote:
| I'm packaging R for Sisyphus repository and package build environment,
| by design, doesn't have /etc/localtime file present. This causes failure
| with Sys.timeone during test run:
[...]
| It seems that the best solution will be to patch Sys.timezone.

The file-based approach was AFAIK never successfully standardized.

Setting a TZ is a defensible fallback.  At some point last year I got so
annoyed about this (and have the historical Debian attitude that a config
file may be preferable to a environment variable [ which I now think is wrong
for some things like TZ ]) I wrote the 'gettz' package.   Quick demo in
a
Docker container with nothing set:

edd at max:~$ docker run --rm -ti r-base /bin/bash
root at f3848979cab4:/# echo $TZ
echo $TZ

root at f3848979cab4:/# R
R

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.getenv("TZ")  # as expected
Sys.getenv("TZ")  # as expected
[1] ""
> install.packages("gettz")
install.packages("gettz")
Installing package into ?/usr/local/lib/R/site-library?
(as ?lib? is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/gettz_0.0.3.tar.gz'
Content type 'application/x-gzip' length 9064 bytes
=================================================downloaded 9064 bytes

* installing *source* package ?gettz? ...
** package ?gettz? successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2
-fdebug-prefix-map=/build/r-base-3.4.0=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gettz.cpp -o
gettz.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o gettz.so gettz.o -L/usr/lib/R/lib
-lR
installing to /usr/local/lib/R/site-library/gettz/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (gettz)

The downloaded source packages are in
	?/tmp/RtmpLvuVz8/downloaded_packages?
> gettz::gettz()
gettz::gettz()
[1] "Etc/UTC"
>

As I recall, R got patched for R 3.3.3 or R 3.4.0 to return "" in more
cases.
gettz is a little smarter about looking in more locations that R was at the
time (and hence not dissimilar to what was suggested earlier today, but
operates at compiled-code level). It uses a trick I found on StackOverflow
(and which is credited in the package).

It is certainly not perfect, but it is "good enough" for the uses I
had in
packages requiring some localtime information.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On Tue, May 16, 2017 at 5:35 PM, Kirill Maslinsky <kirill at altlinux.org>
wrote:
> Hi all,
>
> A problem with tests while building R.
>
> I'm packaging R for Sisyphus repository and package build environment,
> by design, doesn't have /etc/localtime file present. This causes
failure
> with Sys.timeone during test run:
>
> [builder at localhost tests]$ ../bin/R --vanilla < reg-tests-1d.R
>
>> ## PR#17186 - Sys.timezone() on some Debian-derived platforms
>> (S.t <- Sys.timezone())
> Error in normalizePath("/etc/localtime") :
>   (converted from warning) path[1]="/etc/localtime": No such file
or
>   directory
>   Calls: Sys.timezone -> normalizePath
>   Execution halted
>
> This is caused by this code:
>
>> Sys.timezone
> function (location = TRUE)
> {
>     tz <- Sys.getenv("TZ", names = FALSE)
>     if (!location || nzchar(tz))
>         return(Sys.getenv("TZ", unset = NA_character_))
>>>  lt <- normalizePath("/etc/localtime")
> [remainder of the code skkipped]
>
> File /etc/loclatime is optional and is not guaranteed to be present on
> any platform. And anyway, it is a good idea to first check that file
> exists before calling normalizePath.
Looking at the code
(https://github.com/wch/r-source/blob/R-3-4-branch/src/library/base/R/datetime.R#L26),
could it be that mustWork = FALSE (instead of the default NA) avoids
the warning causes this check error?

Index: src/library/base/R/datetime.R
==================================================================---
src/library/base/R/datetime.R (revision 72684)
+++ src/library/base/R/datetime.R (working copy)
@@ -23,7 +23,7 @@
 {
     tz <- Sys.getenv("TZ", names = FALSE)
     if(!location || nzchar(tz)) return(Sys.getenv("TZ", unset =
NA_character_))
-    lt <- normalizePath("/etc/localtime") # Linux, macOS, ...
+    lt <- normalizePath("/etc/localtime", mustWork = FALSE) #
Linux, macOS, ...
     if (grepl(pat <- "^/usr/share/zoneinfo/", lt)) sub(pat,
"", lt)
     else if (lt == "/etc/localtime" &&
file.exists("/etc/timezone") &&
      dir.exists("/usr/share/zoneinfo") &&

/Henrik
>
> Sure, this can be worked around by setting TZ environment variable, but
> that causes tests to fail in another place:
>
> [builder at localhost tests]$ TZ="GMT" ../bin/R --vanilla <
reg-tests-1d.R
>
>> ## format()ing invalid hand-constructed  POSIXlt  objects
>> d <- as.POSIXlt("2016-12-06"); d$zone <- 1
>> tools::assertError(format(d))
> Error: Failed to get error in evaluating format(d)
> Execution halted
>
> It seems that the best solution will be to patch Sys.timezone.
>
> --
> KM
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>
>>>>>     on Tue, 16 May 2017 20:49:02 -0700 writes:
    > On Tue, May 16, 2017 at 5:35 PM, Kirill Maslinsky <kirill at
altlinux.org> wrote:
    >> Hi all,
    >> 
    >> A problem with tests while building R.
    >> 
    >> I'm packaging R for Sisyphus repository and package build
environment,
    >> by design, doesn't have /etc/localtime file present. This
causes failure
    >> with Sys.timeone during test run:
    >> 
    >> [builder at localhost tests]$ ../bin/R --vanilla <
reg-tests-1d.R
    >> 
    >>> ## PR#17186 - Sys.timezone() on some Debian-derived platforms
    >>> (S.t <- Sys.timezone())
    >> Error in normalizePath("/etc/localtime") :
    >> (converted from warning) path[1]="/etc/localtime": No
such file or
    >> directory
    >> Calls: Sys.timezone -> normalizePath
    >> Execution halted
    >> 
    >> This is caused by this code:
    >> 
    >>> Sys.timezone
    >> function (location = TRUE)
    >> {
    >> tz <- Sys.getenv("TZ", names = FALSE)
    >> if (!location || nzchar(tz))
    >> return(Sys.getenv("TZ", unset = NA_character_))
    >>>> lt <- normalizePath("/etc/localtime")
    >> [remainder of the code skkipped]
    >> 
    >> File /etc/loclatime is optional and is not guaranteed to be present
on
    >> any platform. And anyway, it is a good idea to first check that
file
    >> exists before calling normalizePath.

    > Looking at the code
    >
(https://github.com/wch/r-source/blob/R-3-4-branch/src/library/base/R/datetime.R#L26),
    > could it be that mustWork = FALSE (instead of the default NA) avoids
    > the warning causes this check error?

Good idea.

Kirill, could you apply the minimal patch to the sources and
report back ?


    > Index: src/library/base/R/datetime.R
    > ==================================================================   
> --- src/library/base/R/datetime.R (revision 72684)
    > +++ src/library/base/R/datetime.R (working copy)
    > @@ -23,7 +23,7 @@
    > {
    > tz <- Sys.getenv("TZ", names = FALSE)
    > if(!location || nzchar(tz)) return(Sys.getenv("TZ", unset =
NA_character_))
    > -    lt <- normalizePath("/etc/localtime") # Linux, macOS,
...
    > +    lt <- normalizePath("/etc/localtime", mustWork =
FALSE) # Linux, macOS, ...
    > if (grepl(pat <- "^/usr/share/zoneinfo/", lt)) sub(pat,
"", lt)
    > else if (lt == "/etc/localtime" &&
file.exists("/etc/timezone") &&
    > dir.exists("/usr/share/zoneinfo") &&

    > /Henrik

    >> 
    >> Sure, this can be worked around by setting TZ environment variable,
but
    >> that causes tests to fail in another place:
    >> 
    >> [builder at localhost tests]$ TZ="GMT" ../bin/R --vanilla
< reg-tests-1d.R
    >> 
    >>> ## format()ing invalid hand-constructed  POSIXlt  objects
    >>> d <- as.POSIXlt("2016-12-06"); d$zone <- 1
    >>> tools::assertError(format(d))
    >> Error: Failed to get error in evaluating format(d)
    >> Execution halted
    >> 
    >> It seems that the best solution will be to patch Sys.timezone.
    >> 
    >> --
    >> KM
    >> 
    >> ______________________________________________
    >> 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