Hello, I'm having trouble re-submitting a package (graph4lg). - With r-patched_osx, vignette rebuilding fails with the following message : checking re-building of vignette outputs ... [12s/16s] WARNING Error(s) in re-building vignettes: ... --- re-building ?vignette_graph4lg.Rmd? using rmarkdown dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ____chkstk_darwin Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib Error: processing vignette 'vignette_graph4lg.Rmd' failed with diagnostics: pandoc document conversion failed with error 6 --- failed re-building ?vignette_graph4lg.Rmd? SUMMARY: processing the following file failed: ?vignette_graph4lg.Rmd? Error: Vignette re-building failed. Execution halted - Besides, although I removed some unused packages from the imports in DESCRIPTION file, I still obtain this message : checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ?Imap? ?Rdpack? ?ade4? ?doBy? ?mclust? All declared Imports should be used. Except Rdpack which is needed to build the vignette, I removed these packages. Finally, although I submit version 0.4.0, I receive checking errors relative to version 0.3.0. I thank you in advance for your feedbacks. Regards Paul Savary
[R-pkg-devel] Error vignette rebuilding and package imports when re-submitting package
4 messages · Paul SAVARY, Duncan Murdoch, Georgi Boshnakov +1 more
On 15/04/2020 5:14 a.m., Paul SAVARY wrote:
Hello, I'm having trouble re-submitting a package (graph4lg). - With r-patched_osx, vignette rebuilding fails with the following message : checking re-building of vignette outputs ... [12s/16s] WARNING Error(s) in re-building vignettes: ... --- re-building ?vignette_graph4lg.Rmd? using rmarkdown dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ____chkstk_darwin Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib Error: processing vignette 'vignette_graph4lg.Rmd' failed with diagnostics: pandoc document conversion failed with error 6 --- failed re-building ?vignette_graph4lg.Rmd? SUMMARY: processing the following file failed: ?vignette_graph4lg.Rmd? Error: Vignette re-building failed. Execution halted
I was told this was a transient problem on the MacOS build system: the pandoc installed there was defective. I don't know if it has been fixed yet.
- Besides, although I removed some unused packages from the imports in DESCRIPTION file, I still obtain this message : checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ?Imap? ?Rdpack? ?ade4? ?doBy? ?mclust? All declared Imports should be used. Except Rdpack which is needed to build the vignette, I removed these packages.
Generally something needed only for the vignettes should be in Suggests rather than Imports.
Finally, although I submit version 0.4.0, I receive checking errors relative to version 0.3.0.
It sounds like someone slipped up. It might have been you (sending the wrong file, or looking at the wrong check log), or maybe CRAN. In either case, I don't think there's anything you can do other than check that you're submitting the right file (use a new version number) after fixing the Rdpack issue. Duncan Murdoch
I thank you in advance for your feedbacks. Regards Paul Savary [[alternative HTML version deleted]]
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Just add importFrom(Rdpack, reprompt) in the NAMESPACE file (any function from Rdpack will do). Georgi Boshnakov -----Original Message----- From: R-package-devel <r-package-devel-bounces at r-project.org> On Behalf Of Paul SAVARY Sent: 15 April 2020 10:15 To: r-package-devel at r-project.org Subject: [R-pkg-devel] Error vignette rebuilding and package imports when re-submitting package Hello, I'm having trouble re-submitting a package (graph4lg). - With r-patched_osx, vignette rebuilding fails with the following message : checking re-building of vignette outputs ... [12s/16s] WARNING Error(s) in re-building vignettes: ... --- re-building ?vignette_graph4lg.Rmd? using rmarkdown dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ____chkstk_darwin Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib Error: processing vignette 'vignette_graph4lg.Rmd' failed with diagnostics: pandoc document conversion failed with error 6 --- failed re-building ?vignette_graph4lg.Rmd? SUMMARY: processing the following file failed: ?vignette_graph4lg.Rmd? Error: Vignette re-building failed. Execution halted - Besides, although I removed some unused packages from the imports in DESCRIPTION file, I still obtain this message : checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ?Imap? ?Rdpack? ?ade4? ?doBy? ?mclust? All declared Imports should be used. Except Rdpack which is needed to build the vignette, I removed these packages. Finally, although I submit version 0.4.0, I receive checking errors relative to version 0.3.0. I thank you in advance for your feedbacks. Regards Paul Savary ______________________________________________ R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Related thread: https://stat.ethz.ch/pipermail/r-package-devel/2020q2/005300.html best, On Wed, Apr 15, 2020 at 9:13 AM Paul SAVARY <paul.savary at univ-fcomte.fr> wrote:
Hello,
I'm having trouble re-submitting a package (graph4lg).
- With r-patched_osx, vignette rebuilding fails with the following message
:
checking re-building of vignette outputs ... [12s/16s] WARNING
Error(s) in re-building vignettes:
...
--- re-building ?vignette_graph4lg.Rmd? using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X
10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X
10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'vignette_graph4lg.Rmd' failed with
diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ?vignette_graph4lg.Rmd?
SUMMARY: processing the following file failed:
?vignette_graph4lg.Rmd?
Error: Vignette re-building failed.
Execution halted
- Besides, although I removed some unused packages from the imports in
DESCRIPTION file, I still obtain this message :
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
?Imap? ?Rdpack? ?ade4? ?doBy? ?mclust?
All declared Imports should be used.
Except Rdpack which is needed to build the vignette, I removed these
packages.
Finally, although I submit version 0.4.0, I receive checking errors
relative to version 0.3.0.
I thank you in advance for your feedbacks.
Regards
Paul Savary
[[alternative HTML version deleted]]
______________________________________________ R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Fernando Roa [[alternative HTML version deleted]]