From pdalgd at gmail.com  Thu Dec 17 19:30:38 2015
From: pdalgd at gmail.com (peter dalgaard)
Date: Thu, 17 Dec 2015 19:30:38 +0100
Subject: [Rd] Assistance much appreciated
In-Reply-To: <5672F74C.70905@gmail.com>
References: <5672EA93.104@gmail.com> <5672EBB2.5090705@gmail.com>
	<5672F74C.70905@gmail.com>
Message-ID: <651A9020-C94C-4B10-9164-8CC660D13BF0@gmail.com>

Presumably the file in question is one of

Peter-Dalgaards-MacBook-Air:BUILD pd$ grep -r "^Package: tools" *
library/tools/DESCRIPTION:Package: tools
src/library/tools/DESCRIPTION:Package: tools

so the first thing I'd do is to have a good look at those files and see if they got somehow corrupted.

If they look sane, presumably the bit of code that checks it isn't... So that would be my next thing to check.

-pd

> On 17 Dec 2015, at 18:56 , Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> 
> On 17/12/2015 9:06 AM, Michael Felt wrote:
>> More experimenting with calling commands:
>>  > tools:::foobar()
>> Error: Line starting 'Package: tools ...' is malformed!
>>  > tools::foobar()
>> Error: Line starting 'Package: tools ...' is malformed!
> 
> These both do a loadNamespace("tools").
> 
>>  > Tools:::foobar()
>> Error in loadNamespace(name) : there is no package called 'Tools'
>>  > loadNamespace(tools)
>> Error in loadNamespace(tools) : object 'tools' not found
> 
> Those are expected, and unrelated.
> 
>>  > loadNamespace("tools")
>> Error: Line starting 'Package: tools ...' is malformed!
> 
> This shouldn't happen.  In a previous post you listed a long list of warnings about packages not being loaded; that's likely a serious problem, but I don't know if it is the cause or a consequence of this one. Something is seriously wrong with the startup.  You could try debugging setup_Rmainloop in <src/main/main.c>. to see if any warnings are being generated there.  There shouldn't be any.
> 
> Duncan Murdoch
> 
>>  >
>> 
>> 
>> On 17-Dec-15 18:02, Michael Felt wrote:
>>> I have been struggling with this error message - and think I finally
>>> understand it's context.
>>> 
>>> Start
>>> 
>>> Line by line debugging shows me the function works:
>>> 
>>> ...
>>>> saveRDS(val, mapfile)
>>>> val
>>> $variables
>>> $variables$IANA_HTTP_status_code_db
>>> [1]    0 1256
>>> 
>>> $variables$IANA_URI_scheme_db
>>> [1] 1256 3458
>>> 
>>> $variables$table_of_HTTP_status_codes
>>> [1] 4714  830
>>> 
>>> 
>>> $references
>>> named list()
>>> 
>>> $compressed
>>> [1] TRUE
>>> 
>>>> mapfile
>>> [1] "./library/tools/R/sysdata.rdx"
>>>> [1] + Stopped (SIGTSTP)         R_DEFAULT_PACKAGES=NULL LC_ALL=C
>>> ./bin/R --vanilla
>>> root at x065:[/data/prj/cran/64/R-3.2.3]ls -l ./library/tools/R/sysdata.rdx
>>> -rw-r--r--   1 root     33              193 Dec 17 16:49
>>> ./library/tools/R/sysdata.rdx
>>> root at x065:[/data/prj/cran/64/R-3.2.3]cat ./library/tools/R/sysdata.rdx
>>> ?b```b`fbf" SH0#h^?<??@?Al?&_(
>>>                               ??(R?????        ?Y?sS
>>> C7?PG3@??j/D                                        ?aA
>>> OG??x??????????$??X>4?3?89#5IF?$1)'5>?
>>> ?00F??,?(dA1T?(5-?(5/![PZ\2?$?<root at x065:[/data/prj/cran/64/R-3.2.3]
>>> root at x065:[/data/prj/cran/64/R-3.2.3]
>>> root at x065:[/data/prj/cran/64/R-3.2.3]gzip -dc
>>> ./library/tools/R/sysdata.rdx
>>> X
>>> j>      names   IANA_HTTP_status_code_db IANA_URI_scheme_db
>>> table_of_HTTP_status_codes???
>>> ?               variables
>>> references
>>> compressed?root at x065:[/data/prj/cran/64/R-3.2.3]fg
>>>  R_DEFAULT_PACKAGES=NULL LC_ALL=C ./bin/R --vanilla
>>> 
>>>> 
>>>> e
>>> <environment: 110dbf620>
>>>> destDir
>>> [1] "./library/tools/R"
>>>> compress
>>> [1] TRUE
>>>> debug(tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"),
>>> compress = compress))
>>> Error: Line starting 'Package: tools ...' is malformed!
>>>> tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"), compress =
>>> compress)
>>> Error: Line starting 'Package: tools ...' is malformed!
>>>> 
>>> 
>>> So, at the end - my gut-feeling is that the error messages is not
>>> about the arguments, but us related to the "tools:::foo".
>>> 
>>> Where should I look next? It goes a bit beyond me to know where in R
>>> "tools:::foo" is being parsed.
>>> Guessing here - but might be related to the switch from 32-bit to
>>> 64-bit AND that PowerPC is BigEndian rather than LittleEndian? Could
>>> also be absolutely wrong, way off base, etc. --> shoot me down!
>>> 
>>> Thanks,
>>> Michael
>> 
>> ______________________________________________
>> 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

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



[Rd] Assistance much appreciated
peter dalgaard