On 1 February 2021 at 20:21, Jose Barrera wrote:
| Many thanks for your help Thierry but unfortunately I can't see the link
| between your first reply and my issue (of course, that's my fault).
Thierry very gently (yet correctly) suggested to have the "cached" results as
"precomputed"
On 01/02/2021 5:03 p.m., Ulrike Grömping wrote:
Dear package developeRs,
under the Fedora clang checks, I find the note
"Undeclared packages ‘FrF2’, ‘DoE.wrapper’, ‘sfsmisc’, ‘DoE.MIParray’,
‘planor’ in Rd xrefs"
for my package DoE.base. I understand that package planor has been
archived from
So, does that mean that a clean result is contingent on the length of
the data being a multiple of both the number of rows and columns?
However, this rule is not straightforward.
> #EXAMPLE 1
> #what I would expect
> matrix (1:12, 0, 0)
<0 x 0 matrix>
Warning message:
In matrix(1:12, 0, 0) :
That will be hard to do without your package. Note that I've suggested a
work around in my first reply.
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie &
Dear package developeRs,
under the Fedora clang checks, I find the note
"Undeclared packages ‘FrF2’, ‘DoE.wrapper’, ‘sfsmisc’, ‘DoE.MIParray’,
‘planor’ in Rd xrefs"
for my package DoE.base. I understand that package planor has been
archived from CRAN; I don't understand what is wrong with
Many thanks for your help Thierry but unfortunately I can't see the link
between your first reply and my issue (of course, that's my fault).
Jose Barrera
Statistician, Associate Lecturer
*IS**Global*
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research Park (PRBB)
Indeed, the "cache" folder is not present in the tar.gz file. Could you
please help me on how to fix "the cache is not installed into the package"?
Thanks,
Jose Barrera
Statistician, Associate Lecturer
*IS**Global*
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research
Probably because the cache is not installed into the package. I'd check the
tar.gz file to see if the cache is present.
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team
Dear Thierry,
Thanks for your advice. However, I would like to understand why when I
build the vignette to get the pdf from the Rnw, it takes just 8 seconds
once the "cache" folder has been created instead of the initial 4 minutes,
but this time reduction does not happen when checking the
I did a little work in this area, relieving GenomicRanges of dependency on
KEGG.db.
For your example, which does not run (?), I would suggest
a) avoiding the use of the old environments like hgu95av2PATH2PROBE,
replacing
this with AnnotationDbi::select calls
b) replace the KEGG.db invocations
Hi all,
In my package adSplit, I use microarray annotation packages like hgu95av2.db to
find probes for pathways (in hgu95av2PATH2PROBE). In order to find names out of
these KEGG identifiers, I use KEGG.db. However, KEGG.db is deprecated starting
bioconductor 3.13 and bioconductor officials
Hi all,
I have a package under review, ExpHunterSuite. I understand that I must get
the package running with no warnings or errors during the bioconductor
builds before I can go to the next stage of the submission process.
I have achieved this for the linux and Mac builds -
Dear Jose,
I store the results of CPU intensive chunks in the package. Have a look at
https://github.com/ropensci/git2rdata/blob/master/vignettes/efficiency.Rmd.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN
Dear all,
I have an issue when checking a package that includes a vignette using
cache = TRUE in some chunks. The vignette is generated with knit from an
Rnw document. The issue is that cache works when building the vignette
locally but it seems not working when checking the package.
I have
> Abby Spurdle (/əˈbi/)
> on Mon, 1 Feb 2021 19:50:32 +1300 writes:
> I'm a little surprised that the following doesn't trigger an error or a
warning.
> matrix (1:256, 8, 8)
> The help file says that the main argument is recycled, if it's too short.
> But doesn't
On Sun, Jan 31, 2021 at 6:52 PM Duncan Murdoch wrote:
>
> On 31/01/2021 12:35 p.m., Duncan Murdoch wrote:
> > On 31/01/2021 10:57 a.m., Gábor Csárdi wrote:
> >> Do you actually experience any problems, if you don't treat this case
> >> specially?
> >
> > Yes, what was happening was that
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