[Rd] RPostgreSQL installation Error - RPostgreSQL.so: undefined symbol: PQpass
I am trying to install R-Package RPostgreSQL, but getting the following error, Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/RPostgreSQL/libs/RPostgreSQL.so': /usr/lib64/R/library/RPostgreSQL/libs/RPostgreSQL.so: undefined symbol: PQpass Error: loading failed Execution halted ERROR: loading failed * removing â/usr/lib64/R/library/RPostgreSQLâ I have libpq and postgresql-dev installed. All the library files are in the directory /usr/lib64/pgsql/ and all header files are in the directory /usr/include/pgsql/ Postgre Version - 9.3.4 R Version - 3.0.2 Operating System - CentOS-6.4 I am missing some small thing, but unable to find out why this is happening. What am I doing wrong? How to correct this? Thanks and Regards, Manoj g [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] RPostgreSQL installation Error - RPostgreSQL.so: undefined symbol: PQpass
I am trying to install R-Package RPostgreSQL, but getting the following error, Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/RPostgreSQL/libs/RPostgreSQL.so': /usr/lib64/R/library/RPostgreSQL/libs/RPostgreSQL.so: undefined symbol: PQpass Error: loading failed Execution halted ERROR: loading failed * removing â/usr/lib64/R/library/RPostgreSQLâ I have libpq and postgresql-dev installed. All the library files are in the directory /usr/lib64/pgsql/ and all header files are in the directory /usr/include/pgsql/ Postgre Version - 9.3.4 R Version - 3.0.2 Operating System - CentOS-6.4 I am missing some small thing, but unable to find out why this is happening. What am I doing wrong? How to correct this? Thanks and Regards, Manoj G [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Latex errors (build on windows)
I build a R package, however,when I run the"
check("/home/conan/R/chinaWeather") ",
it show me that :
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: File `inconsolata.sty' not found.
Type X to quit or to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
l.281
! ==> Fatal error occurred, no output PDF file produced!
* checking PDF version of manual without hyperrefs or index ... ERROR
and I don't how to solve this PDF version.by the way ,I am not familiar with
Latex,so could anyone tell me how to solve these problem?More thanks!
--
View this message in context:
http://r.789695.n4.nabble.com/Latex-errors-build-on-windows-tp4691118.html
Sent from the R devel mailing list archive at Nabble.com.
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Re: [Rd] citEntry handling of encoded URLs
On Thu, 22 May 2014, Martin Morgan wrote:
The following citEntry includes a url with %3A and other encodings
citEntry(entry="article",
title = "Software for Computing and Annotating Genomic Ranges",
author = personList( as.person("Michael Lawrence" )),
year = 2013,
journal = "{PLoS} Computational Biology",
volume = "9",
issue = "8",
doi = "10.1371/journal.pcbi.1003118",
url =
"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118";,
textVersion = "Lawrence M..." )
Evaluating this as R code doesn't parse correctly and generates a warning
The citEntry (or bibentry) itself is parsed without problem. Some printing
styles cause the warning, specifically when the Rd parser is used for
formatting. Depending on how you want to print it, the warning doesn't
occur though. Using bibentry() directly, we can do:
b <- bibentry("Article",
title = "Software for Computing and Annotating Genomic Ranges",
author = "Michael Lawrence and others",
year = "2013",
journal = "PLoS Comptuational Biology",
volume = "9",
number = "8",
doi = "10.1371/journal.pcbi.1003118",
url =
"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118";,
textVersion = "Lawrence M et al. (2013) ..."
)
Then the default
print(b)
issues a warning because the Rd parser thinks that the % are comments.
However,
print(b, style = "BibTeX")
print(b, style = "citation")
don't issue warnings and also produce output that one might expect.
A work-around is, apparently, to quote the %, \\%3A etc., but is this the
intention?
In that case the default print(b) yields the desired output without
warning but print(b, style = "BibTeX") or print(b, style = "citation") are
possibly not in the desired format. I'm not sure though how the different
BibTeX style files actually handle the URLs. I think some .bst files
handle the "url" field verbatim (i.e., don't need escaping) while others
treat it as text (i.e., need escaping). Personally, I would hence avoid
the problem and only use the DOI URL here as this will be robust across
BibTeX styles.
Nevertheless it is not ideal that there is a discrepancy between the
different printing styles. I think currently this can only be avoided if
custom macros are employed. But Duncan might be able to say more about
this. A similar situation occurs if you use commands that are not part of
the Rd markup, e.g.
n01 <- bibentry("Misc", title = "The $\\mathcal{N}(0, 1)$ Distribution",
author = "Foo Bar", year = "2014")
print(n01) # warning
print(n01, style = "BibTeX") # ok
Also, citEntry points to bibentry points to *Entry Fields*, but the
'url' tag is not mentioned there, even though url appears in the
examples; if the list of supported tags is not easy to enumerate,
perhaps some insight can be provided at this point as to how the
supported tags are determined?
This follows the BibTeX conventions. Thus, you can use any tag that you
wish to use and it will depend on the style whether it is displayed or
not. The only restriction is that certain bibtypes require certain
fields, e.g., an "Article" has to specify: author, title, journal, year.
But beyond that you can add any additional field. For example, in your
bibentry above you used the "issue" field which is ignored by most BibTeX
styles. My adaptation uses the "number" field instead which is processed
by most standard BibTeX styles.
The default print(..., style = "text") uses a bibstyle that is modeled
after jss.bst, the BibTeX style employed by the Journal of Statistical
Software. But you could plug in other .bibstyle arguments, e.g. one that
processes the "issue" field etc.
Hope that helps,
Z
Thanks
Martin Morgan
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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Re: [Rd] Latex errors (build on windows)
On 23/05/2014 12:57, khl0798 wrote:
I build a R package, however,when I run the"
check("/home/conan/R/chinaWeather") ",
it show me that :
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: File `inconsolata.sty' not found.
...
and I don't how to solve this PDF version.by the way ,I am not familiar with
Latex,so could anyone tell me how to solve these problem?More thanks!
Yes, there are people who *could* tell you ... however
*We* write manuals, specifically for Windows
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#LaTeX .
*You* read them. See fortunes::fortune(14)
The posting guide is at http://www.r-project.org/posting-guide.html: you
have not given the 'at a minimum' information required, and we would
also need to know your LaTeX distribution to offer help (although there
are more appropriate LaTeX lists).
Please use your real name when requesting consultancy, as here. R may
be 'free', but advice is costly to those giving it.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] citEntry handling of encoded URLs
On 05/23/2014 05:35 AM, Achim Zeileis wrote:
On Thu, 22 May 2014, Martin Morgan wrote:
The following citEntry includes a url with %3A and other encodings
citEntry(entry="article",
title = "Software for Computing and Annotating Genomic Ranges",
author = personList( as.person("Michael Lawrence" )),
year = 2013,
journal = "{PLoS} Computational Biology",
volume = "9",
issue = "8",
doi = "10.1371/journal.pcbi.1003118",
url =
"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118";,
textVersion = "Lawrence M..." )
Evaluating this as R code doesn't parse correctly and generates a warning
The citEntry (or bibentry) itself is parsed without problem. Some printing
styles cause the warning, specifically when the Rd parser is used for
formatting. Depending on how you want to print it, the warning doesn't occur
though. Using bibentry() directly, we can do:
b <- bibentry("Article",
title = "Software for Computing and Annotating Genomic Ranges",
author = "Michael Lawrence and others",
year = "2013",
journal = "PLoS Comptuational Biology",
volume = "9",
number = "8",
doi = "10.1371/journal.pcbi.1003118",
url =
"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118";,
textVersion = "Lawrence M et al. (2013) ..."
)
Then the default
print(b)
issues a warning because the Rd parser thinks that the % are comments. However,
print(b, style = "BibTeX")
print(b, style = "citation")
don't issue warnings and also produce output that one might expect.
Thanks for clarifying. For what it's worth, I was aiming for
print(b, style="html")
A work-around is, apparently, to quote the %, \\%3A etc., but is this the
intention?
In that case the default print(b) yields the desired output without warning but
print(b, style = "BibTeX") or print(b, style = "citation") are possibly not in
the desired format. I'm not sure though how the different BibTeX style files
actually handle the URLs. I think some .bst files handle the "url" field
verbatim (i.e., don't need escaping) while others treat it as text (i.e., need
escaping). Personally, I would hence avoid the problem and only use the DOI URL
here as this will be robust across BibTeX styles.
Nevertheless it is not ideal that there is a discrepancy between the different
printing styles. I think currently this can only be avoided if custom macros are
employed. But Duncan might be able to say more about this. A similar situation
occurs if you use commands that are not part of the Rd markup, e.g.
n01 <- bibentry("Misc", title = "The $\\mathcal{N}(0, 1)$ Distribution",
author = "Foo Bar", year = "2014")
print(n01) # warning
print(n01, style = "BibTeX") # ok
Also, citEntry points to bibentry points to *Entry Fields*, but the 'url' tag
is not mentioned there, even though url appears in the examples; if the list
of supported tags is not easy to enumerate, perhaps some insight can be
provided at this point as to how the supported tags are determined?
This follows the BibTeX conventions. Thus, you can use any tag that you wish to
use and it will depend on the style whether it is displayed or not. The only
restriction is that certain bibtypes require certain fields, e.g., an "Article"
has to specify: author, title, journal, year. But beyond that you can add any
additional field. For example, in your bibentry above you used the "issue" field
which is ignored by most BibTeX styles. My adaptation uses the "number" field
instead which is processed by most standard BibTeX styles.
The default print(..., style = "text") uses a bibstyle that is modeled after
jss.bst, the BibTeX style employed by the Journal of Statistical Software. But
you could plug in other .bibstyle arguments, e.g. one that processes the "issue"
field etc.
Hope that helps,
Yes, that helps a lot, thanks,
Martin
Z
Thanks
Martin Morgan
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] citEntry handling of encoded URLs
On 23/05/2014 8:35 AM, Achim Zeileis wrote:
On Thu, 22 May 2014, Martin Morgan wrote:
> The following citEntry includes a url with %3A and other encodings
>
> citEntry(entry="article",
> title = "Software for Computing and Annotating Genomic Ranges",
> author = personList( as.person("Michael Lawrence" )),
> year = 2013,
> journal = "{PLoS} Computational Biology",
> volume = "9",
> issue = "8",
> doi = "10.1371/journal.pcbi.1003118",
> url =
>
"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118";,
> textVersion = "Lawrence M..." )
>
> Evaluating this as R code doesn't parse correctly and generates a warning
The citEntry (or bibentry) itself is parsed without problem. Some printing
styles cause the warning, specifically when the Rd parser is used for
formatting. Depending on how you want to print it, the warning doesn't
occur though. Using bibentry() directly, we can do:
b <- bibentry("Article",
title = "Software for Computing and Annotating Genomic Ranges",
author = "Michael Lawrence and others",
year = "2013",
journal = "PLoS Comptuational Biology",
volume = "9",
number = "8",
doi = "10.1371/journal.pcbi.1003118",
url =
"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118";,
textVersion = "Lawrence M et al. (2013) ..."
)
Then the default
print(b)
issues a warning because the Rd parser thinks that the % are comments.
However,
print(b, style = "BibTeX")
print(b, style = "citation")
don't issue warnings and also produce output that one might expect.
> A work-around is, apparently, to quote the %, \\%3A etc., but is this the
> intention?
In that case the default print(b) yields the desired output without
warning but print(b, style = "BibTeX") or print(b, style = "citation") are
possibly not in the desired format. I'm not sure though how the different
BibTeX style files actually handle the URLs. I think some .bst files
handle the "url" field verbatim (i.e., don't need escaping) while others
treat it as text (i.e., need escaping). Personally, I would hence avoid
the problem and only use the DOI URL here as this will be robust across
BibTeX styles.
Nevertheless it is not ideal that there is a discrepancy between the
different printing styles. I think currently this can only be avoided if
custom macros are employed. But Duncan might be able to say more about
this. A similar situation occurs if you use commands that are not part of
the Rd markup, e.g.
I'd go further than "not ideal", I think we need to define what kind of
markup is permissible in this context. If it needs to be Rd markup,
then the default print method should be fixed to hide it (and \mathcal
should not be allowed); if it needs to be plain text, then some escaping
should be done.
n01 <- bibentry("Misc", title = "The $\\mathcal{N}(0, 1)$ Distribution",
author = "Foo Bar", year = "2014")
print(n01) # warning
print(n01, style = "BibTeX") # ok
> Also, citEntry points to bibentry points to *Entry Fields*, but the
> 'url' tag is not mentioned there, even though url appears in the
> examples; if the list of supported tags is not easy to enumerate,
> perhaps some insight can be provided at this point as to how the
> supported tags are determined?
This follows the BibTeX conventions. Thus, you can use any tag that you
wish to use and it will depend on the style whether it is displayed or
not. The only restriction is that certain bibtypes require certain
fields, e.g., an "Article" has to specify: author, title, journal, year.
But beyond that you can add any additional field. For example, in your
bibentry above you used the "issue" field which is ignored by most BibTeX
styles. My adaptation uses the "number" field instead which is processed
by most standard BibTeX styles.
The default print(..., style = "text") uses a bibstyle that is modeled
after jss.bst, the BibTeX style employed by the Journal of Statistical
Software. But you could plug in other .bibstyle arguments, e.g. one that
processes the "issue" field etc.
Hope that helps,
Z
> Thanks
>
> Martin Morgan
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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