stephen sefick
2017-Apr-11 21:47 UTC
[R] colorspace namespace problem with R CMD check --as-cran
I am at a loss. I do not know how to make this reproducible without
providing the package sourced. I am receiving a warning when issuing
R --vanilla CMD check --as-cran --no-restore
The description file has
Imports: methods, reshape2, plyr, doBy, zoo
this is in 00install.out
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: namespace ?colorspace? is not available and has been replaced
by .GlobalEnv when processing object ?plot.index?
Warning: namespace ?colorspace? is not available and has been replaced
by .GlobalEnv when processing object ?plot.index?
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Thank you for any help in advance.
kindest regards,
Stephen Sefick
--
Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make us
feel like gods. We are mammals, and have not exhausted the annoying little
problems of being mammals.
-K. Mullis
"A big computer, a complex algorithm and a long time does not equal
science."
-Robert Gentleman
[[alternative HTML version deleted]]
William Dunlap
2017-Apr-11 22:15 UTC
[R] colorspace namespace problem with R CMD check --as-cran
Does one of the objects in pkg/data (or pkg/R) include a function made
by one of the functions in package:colorspace? Such a function would
have the environment getNamespace("colorspace").
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, Apr 11, 2017 at 2:47 PM, stephen sefick <ssefick at gmail.com>
wrote:> I am at a loss. I do not know how to make this reproducible without
> providing the package sourced. I am receiving a warning when issuing
>
> R --vanilla CMD check --as-cran --no-restore
>
> The description file has
> Imports: methods, reshape2, plyr, doBy, zoo
>
> this is in 00install.out
> ** R
> ** data
> *** moving datasets to lazyload DB
> ** inst
> ** preparing package for lazy loading
> Warning: namespace ?colorspace? is not available and has been replaced
> by .GlobalEnv when processing object ?plot.index?
> Warning: namespace ?colorspace? is not available and has been replaced
> by .GlobalEnv when processing object ?plot.index?
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
>
>
> Thank you for any help in advance.
> kindest regards,
>
> Stephen Sefick
>
> --
> Let's not spend our time and resources thinking about things that are
so
> little or so large that all they really do for us is puff us up and make us
> feel like gods. We are mammals, and have not exhausted the annoying little
> problems of being mammals.
>
> -K. Mullis
>
> "A big computer, a complex algorithm and a long time does not equal
> science."
>
> -Robert Gentleman
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
stephen sefick
2017-Apr-11 23:06 UTC
[R] colorspace namespace problem with R CMD check --as-cran
Thank you for the quick reply. here is what I tried: I used environment(fxn) to look at all of the functions and data in the package. I all of the functions have the namespace of the package. The generic functions have a namespace like <environment: 0x5ea4fc0>. The data loaded with data(pkg_data) have and environment of NULL. colorspace is attached when the package is loaded. Is it possible that a function that I am using from another package is causing this problem?> sessionInfo()R version 3.3.3 (2017-03-06) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Scientific Linux 7.3 (Nitrogen) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] genotypeR_0.0.0.9000 loaded via a namespace (and not attached): [1] zoo_1.7-14 colorspace_1.3-2 MASS_7.3-45 magrittr_1.5 [5] plyr_1.8.4 Matrix_1.2-8 tools_3.3.3 reshape2_1.4.2 [9] Rcpp_0.12.10 stringi_1.1.3 grid_3.3.3 doBy_4.5-15 [13] stringr_1.2.0 lattice_0.20-35 On Tue, Apr 11, 2017 at 5:15 PM, William Dunlap <wdunlap at tibco.com> wrote:> Does one of the objects in pkg/data (or pkg/R) include a function made > by one of the functions in package:colorspace? Such a function would > have the environment getNamespace("colorspace"). > Bill Dunlap > TIBCO Software > wdunlap tibco.com > > > On Tue, Apr 11, 2017 at 2:47 PM, stephen sefick <ssefick at gmail.com> wrote: > > I am at a loss. I do not know how to make this reproducible without > > providing the package sourced. I am receiving a warning when issuing > > > > R --vanilla CMD check --as-cran --no-restore > > > > The description file has > > Imports: methods, reshape2, plyr, doBy, zoo > > > > this is in 00install.out > > ** R > > ** data > > *** moving datasets to lazyload DB > > ** inst > > ** preparing package for lazy loading > > Warning: namespace ?colorspace? is not available and has been replaced > > by .GlobalEnv when processing object ?plot.index? > > Warning: namespace ?colorspace? is not available and has been replaced > > by .GlobalEnv when processing object ?plot.index? > > ** help > > *** installing help indices > > ** building package indices > > ** testing if installed package can be loaded > > > > > > Thank you for any help in advance. > > kindest regards, > > > > Stephen Sefick > > > > -- > > Let's not spend our time and resources thinking about things that are so > > little or so large that all they really do for us is puff us up and make > us > > feel like gods. We are mammals, and have not exhausted the annoying > little > > problems of being mammals. > > > > -K. Mullis > > > > "A big computer, a complex algorithm and a long time does not equal > > science." > > > > -Robert Gentleman > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. >-- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis "A big computer, a complex algorithm and a long time does not equal science." -Robert Gentleman [[alternative HTML version deleted]]
stephen sefick
2017-Apr-11 23:26 UTC
[R] colorspace namespace problem with R CMD check --as-cran
Here is the relevant snippett from devtools::check() logs. I searched every file in pkg/R, and there is no call to plot.index (or plot at all). Warning: namespace ?colorspace? is not available and has been replaced by .GlobalEnv when processing object ?plot.index? Warning: namespace ?colorspace? is not available and has been replaced by .GlobalEnv when processing object ?plot.index? On Tue, Apr 11, 2017 at 5:15 PM, William Dunlap <wdunlap at tibco.com> wrote:> Does one of the objects in pkg/data (or pkg/R) include a function made > by one of the functions in package:colorspace? Such a function would > have the environment getNamespace("colorspace"). > Bill Dunlap > TIBCO Software > wdunlap tibco.com > > > On Tue, Apr 11, 2017 at 2:47 PM, stephen sefick <ssefick at gmail.com> wrote: > > I am at a loss. I do not know how to make this reproducible without > > providing the package sourced. I am receiving a warning when issuing > > > > R --vanilla CMD check --as-cran --no-restore > > > > The description file has > > Imports: methods, reshape2, plyr, doBy, zoo > > > > this is in 00install.out > > ** R > > ** data > > *** moving datasets to lazyload DB > > ** inst > > ** preparing package for lazy loading > > Warning: namespace ?colorspace? is not available and has been replaced > > by .GlobalEnv when processing object ?plot.index? > > Warning: namespace ?colorspace? is not available and has been replaced > > by .GlobalEnv when processing object ?plot.index? > > ** help > > *** installing help indices > > ** building package indices > > ** testing if installed package can be loaded > > > > > > Thank you for any help in advance. > > kindest regards, > > > > Stephen Sefick > > > > -- > > Let's not spend our time and resources thinking about things that are so > > little or so large that all they really do for us is puff us up and make > us > > feel like gods. We are mammals, and have not exhausted the annoying > little > > problems of being mammals. > > > > -K. Mullis > > > > "A big computer, a complex algorithm and a long time does not equal > > science." > > > > -Robert Gentleman > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. >-- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis "A big computer, a complex algorithm and a long time does not equal science." -Robert Gentleman [[alternative HTML version deleted]]