Hello,
When I push my commits to my personal github and they run through TravisCI I
get the following warning when my package ‘clusterExperiment’ is build:
* looking to see if a ‘data/datalist’ file should be added
Warning: namespace ‘clusterExperiment’ is not available and has been replaced
by .GlobalEnv when processing object ‘rsecFluidigm’
(to be clear this warning is saying the namespace of MY package is not
available and the data object it refers to is part of MY package)
I do not get this warning when building on my laptop (where previous versions
of the package are already installed). The warning does not appear anywhere
that I see in R CMD CHECK on TravisCI, just on the build output— I just
discovered it today because I was digging around and reading the successful
build logs on Travis CI). Similarly on the bioconductor check it doesn’t make a
problem with the check (I've cleared bioconductor checks without realizing this
warning was there), but if I go further and read the log of the build on the
bioconductor, the warning is there as well. Given that this wasn’t picked up by
R CMD CHECK, is this something I need be worried about? (I expect the answer
will be yes!) And if so, I would appreciate advice on how to fix it.
I’ve already had problems with this object (‘rsecFluidigm’) breaking my build
when I first added it to the package, and so at that time I set lazyData=false
in my DESCRIPTION file. BEFORE I did this, I would get the following errors (on
my machine not just TravisCI):
** preparing package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace
'S4Vectors'
Also defined by ‘RNeXML’
Error in get0(cname, where, inherits = inherits) :
invalid 'envir' argument
Error in setClassUnion("matrixOrMissing", members = c("matrix", "missing")) :
unable to create union class: could not set members "matrix"
Error in get0(cname, where, inherits = inherits) :
invalid 'envir' argument
Error in setClassUnion("matrixOrMissing", members = c("matrix", "missing")) :
unable to create union class: could not set members "matrix"
Error : unable to load R code in package ‘clusterExperiment’
ERROR: lazy loading failed for package ‘clusterExperiment’
* removing
‘/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjw0000gn/T/Rtmp5LNmph/Rinst1024b4c6db021/clusterExperiment’
I’ve never understood why adding this object to my package created these errors
on lazy load, but lazyData=false seemed to fix the problem, in the sense of
making these errors go away and building the package without problem on both my
machine and Travis CI. Except of course now I realize it’s been giving this
warning on Travis CI without me realizing it. “rsecFluidigm" is a object that
has a class that is created by my package. It’s sole reason for existence is so
that the vignette can be compiled quickly, rather than having to be recreated
while building the vignette (it takes somewhere from 1-5 minutes to recreate
depending on the machine, number of cores, etc.; the vignette has the code to
create it, but with eval=FALSE).
I experimented with also setting lazyLoad=false in my description, but that did
not change anything and I continued to get the warning above.
Here is my description file (minus the collate part):
Package: clusterExperiment
Title: Compare Clusterings for Single-Cell Sequencing
Version: 1.3.7
Description: Provides functionality for running and comparing many
different clusterings of single-cell sequencing data or other large mRNA
Expression data sets.
Authors@R: c(person("Elizabeth", "Purdom", email = "epur...@stat.berkeley.edu",
role = c("aut", "cre", "cph")),
person("Davide","Risso", role = "aut",email =
"risso.dav...@gmail.com"),
person("Marla", "Johnson", role = "ctb"))
Author: Elizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson
[ctb]
Maintainer: Elizabeth Purdom <epur...@stat.berkeley.edu>
BugReports: https://github.com/epurdom/clusterExperiment/issues
License: Artistic-2.0
Depends:
R (>= 3.4),
SummarizedExperiment
Imports:
methods,
NMF,
RColorBrewer,
ape,
phylobase,
cluster,
stats,
limma,
dendextend,
howmany,
locfdr,
matrixStats,
graphics,
parallel,
RSpectra,
kernlab,
stringr
Suggests:
BiocStyle,
knitr,
testthat,
scRNAseq,
MAST
VignetteBuilder: knitr
LazyData: false
RoxygenNote: 6.0.1
biocViews: Clustering, RNASeq, Sequencing, Software, SingleCell
Thanks for any help,
Elizabeth
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