BioC 3.3: CHECK report for genefu on morelia

Package: genefu

Version: 2.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.3.1.tar.gz

StartedAt: 2015-10-22 06:20:29 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 06:22:15 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 105.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genefu.Rcheck

Warnings: 8

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/genefu.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.3.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘survcomp’ ‘mclust’ ‘limma’ ‘biomaRt’ ‘iC10’ ‘AIMS’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genefu’ can be installed ... [11s/12s] WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-3.3-bioc/meat/genefu.Rcheck/00_pkg_src/genefu/man/ihc4.Rd:71: All text must be in a section
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/genefu.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... WARNING
'library' or 'require' call not declared from: ‘impute’
'library' or 'require' call to ‘impute’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘mclust:::grid1’ ‘mclust:::grid2’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
compare:
  function(obj, iC10, newdata, name.test, ...)
compare.proto.cor:
  function(gene.cor, proto.cor, nn, p.adjust.m)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
claudinLow: no visible global function definition for ‘standardize’
claudinLow: no visible binding for global variable ‘bwss’
readarray: no visible global function definition for ‘impute.knn’
Undefined global functions or variables:
  bwss impute.knn standardize
* checking Rd files ... WARNING
prepare_Rd: claudinLow.Rd:44: Dropping empty section \author
prepare_Rd: collapseIDs.Rd:14: Dropping empty section \author
prepare_Rd: ihc4.Rd:71: All text must be in a section
prepare_Rd: medianCtr.Rd:19: Dropping empty section \author
prepare_Rd: overlapSets.Rd:20: Dropping empty section \author
prepare_Rd: readArray.Rd:19: Dropping empty section \author
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Packages unavailable to check Rd xrefs: ‘multilevel’, ‘dplR’
Unknown package ‘claudinLow’ in Rd xrefs
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘claudinLowData’ ‘readarray’
Undocumented data sets:
  ‘claudinLowData’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'medianCtr':
medianCtr
  Code: function(x)
  Docs: function(mat)
  Argument names in code not in docs:
    x
  Argument names in docs not in code:
    mat
  Mismatches in argument names:
    Position: 1 Code: x Docs: mat

Codoc mismatches from documentation object 'overlapSets':
overlapSets
  Code: function(x, y)
  Docs: function(mat1, mat2)
  Argument names in code not in docs:
    x y
  Argument names in docs not in code:
    mat1 mat2
  Mismatches in argument names:
    Position: 1 Code: x Docs: mat1
    Position: 2 Code: y Docs: mat2

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'collapseIDs':
  collapseIDs<-(x,allids=row.names(x),method="mean")
Bad \usage lines found in documentation object 'readArray':
  readarray<-function(dataFile,designFile=NA,hr=1,impute=T,method="mean")

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object 'compare.proto.cor':
  ‘compare.proto.cor’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/14s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 8 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/genefu.Rcheck/00check.log’
for details.

* installing *source* package ‘genefu’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
Warning: /Users/biocbuild/bbs-3.3-bioc/meat/genefu.Rcheck/00_pkg_src/genefu/man/ihc4.Rd:71: All text must be in a section
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefu)

name	user	system	elapsed
bimod	0.271	0.010	0.281
boxplotplus2	0.017	0.000	0.018
claudinLow	1.020	0.028	1.049
compare.proto.cor	0.610	0.014	0.624
compute.pairw.cor.meta	1.012	0.018	1.030
compute.proto.cor.meta	0.402	0.016	0.419
cordiff.dep	0.010	0.002	0.011
endoPredict	0.017	0.001	0.019
expos	0.002	0.000	0.002
fuzzy.ttest	0.002	0.000	0.003
gene70	0.135	0.006	0.142
gene76	0.051	0.001	0.052
geneid.map	0.068	0.003	0.072
genius	0.277	0.004	0.280
ggi	0.048	0.002	0.050
ihc4	0.008	0.003	0.010
intrinsic.cluster	0.247	0.003	0.228
intrinsic.cluster.predict	0.164	0.003	0.168
map.datasets	0.380	0.009	0.389
mod1	0.001	0.001	0.001
mod2	0.001	0.000	0.002
modelOvcAngiogenic	0.002	0.001	0.002
molecular.subtyping	2.107	0.071	2.371
nkis	0.001	0.000	0.002
npi	0.004	0.002	0.007
oncotypedx	0.054	0.001	0.055
ovcAngiogenic	0.059	0.002	0.062
ovcCrijns	0.055	0.001	0.055
ovcTCGA	0.209	0.002	0.213
ovcYoshihara	0.076	0.002	0.079
pam50	0.021	0.001	0.021
pik3cags	0.051	0.001	0.051
power.cor	0.001	0.000	0.001
ps.cluster	0.528	0.013	0.525
read.m.file	0.032	0.002	0.033
rename.duplicate	0.001	0.000	0.002
rescale	0.024	0.003	0.027
rorS	0.118	0.002	0.120
scmgene.robust	0.003	0.000	0.003
scmod1.robust	0.005	0.001	0.005
scmod2.robust	0.006	0.000	0.007
setcolclass.df	0.002	0.000	0.003
sig.endoPredict	0.003	0.000	0.003
sig.gene70	0.005	0.001	0.005
sig.gene76	0.007	0.001	0.008
sig.genius	0.034	0.005	0.038
sig.ggi	0.005	0.000	0.005
sig.oncotypedx	0.003	0.001	0.003
sig.pik3cags	0.003	0.000	0.003
sig.score	0.055	0.003	0.058
sig.tamr13	0.004	0.001	0.005
sigOvcAngiogenic	0.005	0.000	0.006
sigOvcCrijns	0.008	0.001	0.008
sigOvcSpentzos	0.008	0.001	0.008
sigOvcTCGA	0.010	0.001	0.011
sigOvcYoshihara	0.005	0.000	0.005
spearmanCI	0.001	0.001	0.001
ssp2003	0.026	0.001	0.027
ssp2006	0.029	0.002	0.030
st.gallen	0.010	0.002	0.044
stab.fs	0.140	0.005	0.144
stab.fs.ranking	0.820	0.022	0.841
strescR	0.001	0.000	0.001
subtype.cluster	0.342	0.021	0.365
subtype.cluster.predict	0.113	0.003	0.117
tamr13	0.043	0.002	0.045
tbrm	0.001	0.000	0.001
vdxs	0.002	0.001	0.002
weighted.meanvar	0.001	0.000	0.001
write.m.file	0.002	0.001	0.003