From: "Luca De Sano" <l.desano at campus.unimib.it>
To: "Vincent Carey" <stvjc at channing.harvard.edu>
Cc: "bioc-devel" <bioc-devel at r-project.org>
Sent: Thursday, February 25, 2016 7:56:58 AM
Subject: Re: [Bioc-devel] R CMD check problems
The problem is that the NAMESPACE is regenerated every time I execute the
document() command.
At the moment, in the description file I've added bnlean
Depends:
R (>= 3.1),
bnlearn,
doParallel,
to prevent this:
library(devtools)
document()
Updating TRONCO documentation
Loading TRONCO
Loading required package: doParallel
Loading required package: foreach
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com
Loading required package: iterators
Loading required package: parallel
Warning messages:
1: .onLoad failed in loadNamespace() for 'bnlearn', details:
call: setMethod("nodes", cl, function(object) .nodes(object))
error: no existing definition for function ?nodes?
2: .onLoad failed in loadNamespace() for 'bnlearn', details:
call: setMethod("nodes", cl, function(object) .nodes(object))
error: no existing definition for function ?nodes?
3: .onLoad failed in loadNamespace() for 'bnlearn', details:
call: setMethod("nodes", cl, function(object) .nodes(object))
error: no existing definition for function ?nodes?
4: .onLoad failed in loadNamespace() for 'bnlearn', details:
call: setMethod("nodes", cl, function(object) .nodes(object))
error: no existing definition for function ?nodes?
With this configuration I can build and check the package, but the warnings
mentioned above still remain.
--
Luca De Sano
tel: +393337177338
email: l.desano at campus.unimib.it
PEC: luca.desano at pec.it
On 25 February 2016 at 16:23, Vincent Carey <stvjc at channing.harvard.edu>
wrote:
I am evidently not expert in this topic. However I was able to get past
the warning/halt you identified by moving the importFrom(bnlearn,...)
statements to the top of the NAMESPACE. I cannot see in the WRE manual how
the order of namespace imports/exports should be controlled. Other minds
will be needed to set this straight.
On Thu, Feb 25, 2016 at 6:06 AM, Luca De Sano <l.desano at campus.unimib.it>
wrote:
This is my sessionInfo(), I've the current stable release of bnlearn
(3.9).
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] TRONCO_2.4.0 bnlearn_3.9 doParallel_1.0.10 iterators_1.0.8
[5] foreach_1.4.3 devtools_1.10.0
loaded via a namespace (and not attached):
[1] igraph_1.0.1 graph_1.44.1 Rcpp_0.12.3
[4] magrittr_1.5 roxygen2_5.0.1 BiocGenerics_0.12.1
[7] munsell_0.4.3 xtable_1.8-2 colorspace_1.2-6
[10] stringr_1.0.0 plyr_1.8.3 tools_3.2.3
[13] grid_3.2.3 gtable_0.1.2 R.oo_1.20.0
[16] withr_1.0.1 digest_0.6.9 gridExtra_2.0.0
[19] RColorBrewer_1.1-2 Rgraphviz_2.10.0 reshape2_1.4.1
[22] ggplot2_2.0.0 cgdsr_1.2.5 codetools_0.2-14
[25] memoise_1.0.0 stringi_1.0-1 R.methodsS3_1.7.1
[28] scales_0.3.0 stats4_3.2.3
--
Luca De Sano
tel: +393337177338
email: l.desano at campus.unimib.it
PEC: luca.desano at pec.it
On 25 February 2016 at 12:03, Vincent Carey <stvjc at channing.harvard.edu>
wrote:
sessionInfo might help. my guess is that you have an outofdate bnlearn
installed?
On Thu, Feb 25, 2016 at 5:57 AM, Luca De Sano <l.desano at campus.unimib.it
Hi all,
I'm working on a package named TRONCO (
http://bioconductor.org/packages/devel/bioc/html/TRONCO.html ) which
was
released last year on bioconductor. Everytime I run R CMD check I get
these
two warnings:
* checking whether the namespace can be loaded with stated dependencies
...
WARNING
Error: .onLoad failed in loadNamespace() for 'bnlearn', details:
call: setMethod("nodes", cl, function(object) .nodes(object))
error: no existing definition for function ?nodes?
Execution halted
* checking whether the namespace can be unloaded cleanly ... WARNING
Error: .onLoad failed in loadNamespace() for 'bnlearn', details:
call: setMethod("nodes", cl, function(object) .nodes(object))
error: no existing definition for function ?nodes?
Execution halted
I've searched informations about these errors and I've only found some
old
posts on StackOverflow which suggested to change the order of the
import.
I've tried to do it with no result. At the moment I can't figure out
what
those warnings mean!
Any suggestions?
Warnings can be reproduced with the code listed below:
git clone https://github.com/BIMIB-DISCo/TRONCO.git
R CMD build TRONCO
R CMD check TRONCO_2.3.0.tar.gz
Thank you
--
Luca De Sano
tel: +393337177338
email: l.desano at campus.unimib.it
PEC: luca.desano at pec.it
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