[Bioc-devel] Warning that namespace of my package not available for my data object

[Elizabeth Purdom]

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Warning: namespace ‘clusterExperiment’ is not available and has been replaced
by .GlobalEnv when processing object ‘rsecFluidigm’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 at R: c(person("Elizabeth", "Purdom", email = "epurdom at stat.berkeley.edu",
            role = c("aut", "cre", "cph")),
	     person("Davide","Risso", role = "aut",email = "risso.davide at gmail.com"),
	     person("Marla", "Johnson", role = "ctb"))
Author: Elizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb]
Maintainer: Elizabeth Purdom <epurdom at 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