William Dunlap
2009-Oct-22 20:53 UTC
[Rd] Error in link in Rd file stops package installation
With a pretty recent version of R 2.11.0 (devel,unstable,
svn 50178) on Linux I could not install version 1.5-8 of zoo (the
current on on CRAN):
% R-devel CMD INSTALL -l Rlib3 zoo
* installing *source* package 'zoo' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'zoo'
finding HTML links ... done
MATCH html
ORDER html
aggregate.zoo html
as.Date.ts html
as.zoo html
coredata html
frequency html
index html
is.regular html
lag.zoo html
Error: argument is of length zero
* removing
'/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
The tryCatch calls in the installer code obliterate
most traces of where this 'argument is of length zero'
comes from. If I run the install from a directory containing
the .Rprofile file containing the line
utils::assignInNamespace("tryCatch", function(expr, ...) expr,
ns="base")
then I get:
...
is.regular html
lag.zoo html Error in if
(nzchar(file)) { : argument is of length zero
* removing
'/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
* restoring previous
'/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
and I can grep around for 'if (nzchar(file))'. (Redefining q() in
.Rprofile to give a traceback can help in the search also.)
After the attached change to Rd2HTML I get
...
index html
is.regular html
lag.zoo html
Rd warning: ./man/lag.zoo.Rd:54: missing file link 'diff'
make.par.list html
merge.zoo html
...
Line 54 of that help file is
\seealso{\code{\link{zoo}}, \code{\link[stats]{lag}},
\code{\link[stats]{diff}}}
and I think the [stats]{diff} should be [base]{diff}.
The change I made (which isn't quite right but avoids
mysteriously killing the installation for what turns out
to be a minor error) was
Index: src/library/tools/R/Rd2HTML.R
==================================================================---
src/library/tools/R/Rd2HTML.R (revision 50178)
+++ src/library/tools/R/Rd2HTML.R (working copy)
@@ -305,7 +305,7 @@
if (!OK) {
## so how about as a topic?
file <- utils:::index.search(parts$targetfile,
pkgpath)
- if (nzchar(file)) {
+ if (length(file)>0 && nzchar(file)) {
warnRd(block, Rdfile,
"file link ",
sQuote(parts$targetfile),
" in package ", sQuote(parts$pkg),
A longer range fix would be to print more contextual
information with the error messages from INSTALL.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
William Dunlap
2009-Oct-23 03:03 UTC
[Rd] Error in link in Rd file stops package installation
The following patch seems to get the warning message right
lag.zoo html
Rd warning: ./man/lag.zoo.Rd:54: file link 'diff' in package
'stats'
does not exist and so has been treated as a topic
Index: src/library/tools/R/Rd2HTML.R
==================================================================---
src/library/tools/R/Rd2HTML.R (revision 50178)
+++ src/library/tools/R/Rd2HTML.R (working copy)
@@ -305,7 +305,7 @@
if (!OK) {
## so how about as a topic?
file <- utils:::index.search(parts$targetfile,
pkgpath)
- if (nzchar(file)) {
+ if (length(file)==0 || nzchar(file)) {
warnRd(block, Rdfile,
"file link ",
sQuote(parts$targetfile),
" in package ", sQuote(parts$pkg),
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -----Original Message-----
> From: r-devel-bounces at r-project.org
> [mailto:r-devel-bounces at r-project.org] On Behalf Of William Dunlap
> Sent: Thursday, October 22, 2009 1:54 PM
> To: R-devel at r-project.org
> Subject: [Rd] Error in link in Rd file stops package installation
>
> With a pretty recent version of R 2.11.0 (devel,unstable,
> svn 50178) on Linux I could not install version 1.5-8 of zoo (the
> current on on CRAN):
>
> % R-devel CMD INSTALL -l Rlib3 zoo
> * installing *source* package 'zoo' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> converting help for package 'zoo'
> finding HTML links ... done
> MATCH html
> ORDER html
> aggregate.zoo html
> as.Date.ts html
> as.zoo html
> coredata html
> frequency html
> index html
> is.regular html
> lag.zoo html
> Error: argument is of length zero
> * removing
> '/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
>
> The tryCatch calls in the installer code obliterate
> most traces of where this 'argument is of length zero'
> comes from. If I run the install from a directory containing
> the .Rprofile file containing the line
> utils::assignInNamespace("tryCatch", function(expr, ...) expr,
> ns="base")
> then I get:
> ...
> is.regular html
> lag.zoo html Error in if
> (nzchar(file)) { : argument is of length zero
> * removing
> '/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
> * restoring previous
> '/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
> and I can grep around for 'if (nzchar(file))'. (Redefining q() in
> .Rprofile to give a traceback can help in the search also.)
>
> After the attached change to Rd2HTML I get
> ...
> index html
> is.regular html
> lag.zoo html
> Rd warning: ./man/lag.zoo.Rd:54: missing file link 'diff'
> make.par.list html
> merge.zoo html
> ...
> Line 54 of that help file is
> \seealso{\code{\link{zoo}}, \code{\link[stats]{lag}},
> \code{\link[stats]{diff}}}
> and I think the [stats]{diff} should be [base]{diff}.
>
> The change I made (which isn't quite right but avoids
> mysteriously killing the installation for what turns out
> to be a minor error) was
>
> Index: src/library/tools/R/Rd2HTML.R
> ==================================================================> ---
src/library/tools/R/Rd2HTML.R (revision 50178)
> +++ src/library/tools/R/Rd2HTML.R (working copy)
> @@ -305,7 +305,7 @@
> if (!OK) {
> ## so how about as a topic?
> file <- utils:::index.search(parts$targetfile,
> pkgpath)
> - if (nzchar(file)) {
> + if (length(file)>0 && nzchar(file)) {
> warnRd(block, Rdfile,
> "file link ",
> sQuote(parts$targetfile),
> " in package ",
sQuote(parts$pkg),
>
> A longer range fix would be to print more contextual
> information with the error messages from INSTALL.
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
> ______________________________________________
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>