BioC 2.14: CHECK report for KEGGSOAP on zin2

Package: KEGGSOAP

Version: 1.35.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings --no-examples KEGGSOAP_1.35.0.tar.gz

StartedAt: 2013-10-08 00:58:02 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 00:58:53 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 51.4 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGSOAP.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/KEGGSOAP.Rcheck’
* using R Under development (unstable) (2013-10-02 r64018)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-examples --no-vignettes’
* checking for file ‘KEGGSOAP/DESCRIPTION’ ... OK
* this is package ‘KEGGSOAP’ version ‘1.35.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘KEGGSOAP’ can be installed ... [3s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Deprecated license: BSD
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘XMLSchema’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages needs to imported from for the case when
  this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘KEGGSOAP/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste(msg, collapse = "\n"))

See section ‘Good practice’ in '?.onAttach'.

bconv: no visible binding for global variable ‘KEGGserver’
bconv: no visible binding for global variable ‘KEGGaction’
bconv: no visible binding for global variable ‘KEGGxmlns’
bconv: no visible binding for global variable ‘KEGGsoapns’
bget: no visible binding for global variable ‘KEGGserver’
bget: no visible binding for global variable ‘KEGGaction’
bget: no visible binding for global variable ‘KEGGxmlns’
bget: no visible binding for global variable ‘KEGGsoapns’
color.pathway.by.objects: no visible binding for global variable
  ‘KEGGIFace’
color.pathway.by.objects: no visible binding for global variable
  ‘KEGGserver’
color.pathway.by.objects: no visible binding for global variable
  ‘KEGGaction’
color.pathway.by.objects: no visible binding for global variable
  ‘KEGGxmlns’
color.pathway.by.objects: no visible binding for global variable
  ‘KEGGsoapns’
get.compounds.by.pathway: no visible binding for global variable
  ‘KEGGserver’
get.compounds.by.pathway: no visible binding for global variable
  ‘KEGGaction’
get.compounds.by.pathway: no visible binding for global variable
  ‘KEGGxmlns’
get.compounds.by.pathway: no visible binding for global variable
  ‘KEGGsoapns’
get.enzymes.by.pathway: no visible binding for global variable
  ‘KEGGserver’
get.enzymes.by.pathway: no visible binding for global variable
  ‘KEGGaction’
get.enzymes.by.pathway: no visible binding for global variable
  ‘KEGGxmlns’
get.enzymes.by.pathway: no visible binding for global variable
  ‘KEGGsoapns’
get.genes.by.ko: no visible binding for global variable ‘KEGGserver’
get.genes.by.ko: no visible binding for global variable ‘KEGGaction’
get.genes.by.ko: no visible binding for global variable ‘KEGGxmlns’
get.genes.by.ko: no visible binding for global variable ‘KEGGsoapns’
get.genes.by.ko.class: no visible binding for global variable
  ‘KEGGserver’
get.genes.by.ko.class: no visible binding for global variable
  ‘KEGGaction’
get.genes.by.ko.class: no visible binding for global variable
  ‘KEGGxmlns’
get.genes.by.ko.class: no visible binding for global variable
  ‘KEGGsoapns’
get.genes.by.motifs: no visible binding for global variable
  ‘KEGGserver’
get.genes.by.motifs: no visible binding for global variable
  ‘KEGGaction’
get.genes.by.motifs: no visible binding for global variable ‘KEGGxmlns’
get.genes.by.motifs: no visible binding for global variable
  ‘KEGGsoapns’
get.genes.by.organism: no visible binding for global variable
  ‘KEGGserver’
get.genes.by.organism: no visible binding for global variable
  ‘KEGGaction’
get.genes.by.organism: no visible binding for global variable
  ‘KEGGxmlns’
get.genes.by.organism: no visible binding for global variable
  ‘KEGGsoapns’
get.genes.by.pathway: no visible binding for global variable
  ‘KEGGserver’
get.genes.by.pathway: no visible binding for global variable
  ‘KEGGaction’
get.genes.by.pathway: no visible binding for global variable
  ‘KEGGxmlns’
get.genes.by.pathway: no visible binding for global variable
  ‘KEGGsoapns’
get.ko.by.gene: no visible binding for global variable ‘KEGGserver’
get.ko.by.gene: no visible binding for global variable ‘KEGGaction’
get.ko.by.gene: no visible binding for global variable ‘KEGGxmlns’
get.ko.by.gene: no visible binding for global variable ‘KEGGsoapns’
get.ko.by.ko.class: no visible binding for global variable ‘KEGGserver’
get.ko.by.ko.class: no visible binding for global variable ‘KEGGaction’
get.ko.by.ko.class: no visible binding for global variable ‘KEGGxmlns’
get.ko.by.ko.class: no visible binding for global variable ‘KEGGsoapns’
get.kos.by.pathway: no visible binding for global variable ‘KEGGserver’
get.kos.by.pathway: no visible binding for global variable ‘KEGGaction’
get.kos.by.pathway: no visible binding for global variable ‘KEGGxmlns’
get.kos.by.pathway: no visible binding for global variable ‘KEGGsoapns’
get.motifs.by.gene: no visible binding for global variable ‘KEGGserver’
get.motifs.by.gene: no visible binding for global variable ‘KEGGaction’
get.motifs.by.gene: no visible binding for global variable ‘KEGGxmlns’
get.motifs.by.gene: no visible binding for global variable ‘KEGGsoapns’
get.paralogs.by.gene: no visible binding for global variable
  ‘KEGGserver’
get.paralogs.by.gene: no visible binding for global variable
  ‘KEGGaction’
get.paralogs.by.gene: no visible binding for global variable
  ‘KEGGxmlns’
get.paralogs.by.gene: no visible binding for global variable
  ‘KEGGsoapns’
get.pathways.by.compounds: no visible binding for global variable
  ‘KEGGIFace’
get.pathways.by.compounds: no visible binding for global variable
  ‘KEGGserver’
get.pathways.by.compounds: no visible binding for global variable
  ‘KEGGaction’
get.pathways.by.compounds: no visible binding for global variable
  ‘KEGGxmlns’
get.pathways.by.compounds: no visible binding for global variable
  ‘KEGGsoapns’
get.pathways.by.enzymes: no visible binding for global variable
  ‘KEGGIFace’
get.pathways.by.enzymes: no visible binding for global variable
  ‘KEGGserver’
get.pathways.by.enzymes: no visible binding for global variable
  ‘KEGGaction’
get.pathways.by.enzymes: no visible binding for global variable
  ‘KEGGxmlns’
get.pathways.by.enzymes: no visible binding for global variable
  ‘KEGGsoapns’
get.pathways.by.genes: no visible binding for global variable
  ‘KEGGIFace’
get.pathways.by.genes: no visible binding for global variable
  ‘KEGGserver’
get.pathways.by.genes: no visible binding for global variable
  ‘KEGGaction’
get.pathways.by.genes: no visible binding for global variable
  ‘KEGGxmlns’
get.pathways.by.genes: no visible binding for global variable
  ‘KEGGsoapns’
get.pathways.by.kos: no visible binding for global variable
  ‘KEGGserver’
get.pathways.by.kos: no visible binding for global variable
  ‘KEGGaction’
get.pathways.by.kos: no visible binding for global variable ‘KEGGxmlns’
get.pathways.by.kos: no visible binding for global variable
  ‘KEGGsoapns’
get.pathways.by.reactions: no visible binding for global variable
  ‘KEGGIFace’
get.pathways.by.reactions: no visible binding for global variable
  ‘KEGGserver’
get.pathways.by.reactions: no visible binding for global variable
  ‘KEGGaction’
get.pathways.by.reactions: no visible binding for global variable
  ‘KEGGxmlns’
get.pathways.by.reactions: no visible binding for global variable
  ‘KEGGsoapns’
get.reactions.by.pathway: no visible binding for global variable
  ‘KEGGserver’
get.reactions.by.pathway: no visible binding for global variable
  ‘KEGGaction’
get.reactions.by.pathway: no visible binding for global variable
  ‘KEGGxmlns’
get.reactions.by.pathway: no visible binding for global variable
  ‘KEGGsoapns’
getBestNeighbors: no visible binding for global variable ‘KEGGserver’
getBestNeighbors: no visible binding for global variable ‘KEGGaction’
getBestNeighbors: no visible binding for global variable ‘KEGGxmlns’
getBestNeighbors: no visible binding for global variable ‘KEGGsoapns’
list.databases: no visible binding for global variable ‘KEGGserver’
list.databases: no visible binding for global variable ‘KEGGaction’
list.databases: no visible binding for global variable ‘KEGGxmlns’
list.databases: no visible binding for global variable ‘KEGGsoapns’
list.organisms: no visible binding for global variable ‘KEGGserver’
list.organisms: no visible binding for global variable ‘KEGGaction’
list.organisms: no visible binding for global variable ‘KEGGxmlns’
list.organisms: no visible binding for global variable ‘KEGGsoapns’
list.pathways: no visible binding for global variable ‘KEGGserver’
list.pathways: no visible binding for global variable ‘KEGGaction’
list.pathways: no visible binding for global variable ‘KEGGxmlns’
list.pathways: no visible binding for global variable ‘KEGGsoapns’
mark.pathway.by.objects: no visible binding for global variable
  ‘KEGGIFace’
mark.pathway.by.objects: no visible binding for global variable
  ‘KEGGserver’
mark.pathway.by.objects: no visible binding for global variable
  ‘KEGGaction’
mark.pathway.by.objects: no visible binding for global variable
  ‘KEGGxmlns’
mark.pathway.by.objects: no visible binding for global variable
  ‘KEGGsoapns’
search.compounds.by.composition: no visible binding for global variable
  ‘KEGGserver’
search.compounds.by.composition: no visible binding for global variable
  ‘KEGGaction’
search.compounds.by.composition: no visible binding for global variable
  ‘KEGGxmlns’
search.compounds.by.composition: no visible binding for global variable
  ‘KEGGsoapns’
search.compounds.by.mass: no visible binding for global variable
  ‘KEGGserver’
search.compounds.by.mass: no visible binding for global variable
  ‘KEGGaction’
search.compounds.by.mass: no visible binding for global variable
  ‘KEGGxmlns’
search.compounds.by.mass: no visible binding for global variable
  ‘KEGGsoapns’
search.compounds.by.name: no visible binding for global variable
  ‘KEGGserver’
search.compounds.by.name: no visible binding for global variable
  ‘KEGGaction’
search.compounds.by.name: no visible binding for global variable
  ‘KEGGxmlns’
search.compounds.by.name: no visible binding for global variable
  ‘KEGGsoapns’
search.compounds.by.subcomp: no visible binding for global variable
  ‘KEGGserver’
search.compounds.by.subcomp: no visible binding for global variable
  ‘KEGGaction’
search.compounds.by.subcomp: no visible binding for global variable
  ‘KEGGxmlns’
search.compounds.by.subcomp: no visible binding for global variable
  ‘KEGGsoapns’
search.glycans.by.composition: no visible binding for global variable
  ‘KEGGserver’
search.glycans.by.composition: no visible binding for global variable
  ‘KEGGaction’
search.glycans.by.composition: no visible binding for global variable
  ‘KEGGxmlns’
search.glycans.by.composition: no visible binding for global variable
  ‘KEGGsoapns’
search.glycans.by.kcam: no visible binding for global variable
  ‘KEGGserver’
search.glycans.by.kcam: no visible binding for global variable
  ‘KEGGaction’
search.glycans.by.kcam: no visible binding for global variable
  ‘KEGGxmlns’
search.glycans.by.kcam: no visible binding for global variable
  ‘KEGGsoapns’
search.glycans.by.mass: no visible binding for global variable
  ‘KEGGserver’
search.glycans.by.mass: no visible binding for global variable
  ‘KEGGaction’
search.glycans.by.mass: no visible binding for global variable
  ‘KEGGxmlns’
search.glycans.by.mass: no visible binding for global variable
  ‘KEGGsoapns’
search.glycans.by.name: no visible binding for global variable
  ‘KEGGserver’
search.glycans.by.name: no visible binding for global variable
  ‘KEGGaction’
search.glycans.by.name: no visible binding for global variable
  ‘KEGGxmlns’
search.glycans.by.name: no visible binding for global variable
  ‘KEGGsoapns’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/KEGGSOAP.Rcheck/00check.log’
for details.

* installing *source* package ‘KEGGSOAP’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (KEGGSOAP)