BioC 3.3: CHECK report for genefu on morelia

Package: genefu

Version: 2.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.3.2.tar.gz

StartedAt: 2016-04-21 02:50:12 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 02:53:27 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 195.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genefu.Rcheck

Warnings: 5

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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_2.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/genefu.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘2.3.2’
* 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 ... [18s/19s] OK
* 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
.ovcSigs: no visible global function definition for ‘read.csv’
bimod: no visible global function definition for ‘complete.cases’
boxplotplus2: no visible global function definition for ‘boxplot’
boxplotplus2: no visible global function definition for ‘points’
claudinLow: no visible global function definition for ‘standardize’
claudinLow: no visible binding for global variable ‘bwss’
claudinLow: no visible global function definition for ‘dist’
claudinLow: no visible global function definition for ‘cor’
collapseIDs: no visible binding for global variable ‘median’
collapseIDs: no visible binding for global variable ‘sd’
collapseIDs : <anonymous>: no visible global function definition for
  ‘quantile’
compare.proto.cor: no visible global function definition for ‘p.adjust’
compute.pairw.cor.meta: no visible global function definition for ‘cor’
compute.pairw.cor.meta: no visible global function definition for
  ‘complete.cases’
compute.pairw.cor.z: no visible global function definition for ‘cor’
compute.pairw.cor.z: no visible global function definition for
  ‘complete.cases’
compute.proto.cor.meta : <anonymous>: no visible global function
  definition for ‘complete.cases’
compute.proto.cor.meta : <anonymous>: no visible global function
  definition for ‘cor’
compute.proto.cor.meta: no visible global function definition for
  ‘complete.cases’
compute.proto.cor.meta: no visible global function definition for ‘cor’
cordiff.dep: no visible global function definition for ‘pt’
endoPredict : <anonymous>: no visible global function definition for
  ‘quantile’
fuzzy.ttest: no visible global function definition for ‘complete.cases’
fuzzy.ttest: no visible global function definition for ‘pt’
gene70 : <anonymous>: no visible global function definition for
  ‘complete.cases’
gene70 : <anonymous>: no visible global function definition for ‘cor’
geneid.map: no visible binding for global variable ‘sd’
ihc4: no visible global function definition for ‘complete.cases’
intrinsic.cluster: no visible global function definition for ‘cutree’
intrinsic.cluster: no visible binding for global variable ‘median’
intrinsic.cluster : <anonymous>: no visible global function definition
  for ‘cor’
intrinsic.cluster: no visible global function definition for
  ‘write.table’
intrinsic.cluster.predict: no visible global function definition for
  ‘read.csv’
intrinsic.cluster.predict : <anonymous>: no visible global function
  definition for ‘complete.cases’
intrinsic.cluster.predict : <anonymous>: no visible global function
  definition for ‘cor’
intrinsic.cluster.predict: no visible global function definition for
  ‘cutree’
intrinsic.cluster.predict: no visible binding for global variable
  ‘median’
medianCtr: no visible binding for global variable ‘median’
molecular.subtyping: no visible binding for global variable ‘gt’
molecular.subtyping: no visible binding for global variable ‘verbose’
molecular.subtyping : <anonymous>: no visible global function
  definition for ‘complete.cases’
molecular.subtyping : <anonymous>: no visible global function
  definition for ‘cor’
molecular.subtyping: no visible binding for global variable
  ‘method.cor’
npi: no visible global function definition for ‘complete.cases’
oncotypedx: no visible global function definition for ‘complete.cases’
ovcCrijns: no visible global function definition for ‘median’
ovcTCGA : <anonymous>: no visible global function definition for
  ‘t.test’
ovcYoshihara: no visible global function definition for ‘median’
power.cor: no visible global function definition for ‘qnorm’
ps.cluster: no visible global function definition for ‘complete.cases’
read.m.file: no visible global function definition for ‘read.csv’
readarray: no visible global function definition for ‘read.table’
readarray: no visible global function definition for ‘impute.knn’
rescale: no visible global function definition for ‘quantile’
rorS: no visible global function definition for ‘quantile’
spearmanCI: no visible global function definition for ‘qnorm’
spearmanCI: no visible global function definition for ‘pnorm’
st.gallen: no visible global function definition for ‘complete.cases’
subtype.cluster: no visible global function definition for
  ‘complete.cases’
subtype.cluster: no visible global function definition for ‘median’
subtype.cluster: no visible global function definition for ‘par’
subtype.cluster: no visible global function definition for ‘persp’
subtype.cluster: no visible global function definition for ‘pnorm’
subtype.cluster: no visible global function definition for ‘legend’
subtype.cluster.predict: no visible global function definition for
  ‘complete.cases’
subtype.cluster.predict: no visible global function definition for
  ‘median’
subtype.cluster.predict: no visible global function definition for
  ‘pnorm’
subtype.cluster.predict: no visible global function definition for
  ‘legend’
tbrm: no visible global function definition for ‘median’
weighted.meanvar: no visible global function definition for
  ‘complete.cases’
write.m.file: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot bwss complete.cases cor cutree dist gt impute.knn legend
  median method.cor p.adjust par persp pnorm points pt qnorm quantile
  read.csv read.table sd standardize t.test verbose write.table
Consider adding
  importFrom("graphics", "boxplot", "legend", "par", "persp", "points")
  importFrom("stats", "complete.cases", "cor", "cutree", "dist",
             "median", "p.adjust", "pnorm", "pt", "qnorm", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* 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:
  ‘readarray’
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 ... OK
* 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 ... [23s/24s] 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: 5 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
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefu)

name	user	system	elapsed
bimod	0.420	0.020	0.443
boxplotplus2	0.011	0.001	0.013
claudinLow	0.992	0.026	1.022
claudinLowData	0.150	0.124	0.276
compare.proto.cor	0.948	0.021	0.989
compute.pairw.cor.meta	1.367	0.037	1.429
compute.proto.cor.meta	0.717	0.024	0.783
cordiff.dep	0.014	0.004	0.018
endoPredict	0.021	0.005	0.027
expos	0.002	0.001	0.004
fuzzy.ttest	0.002	0.000	0.003
gene70	0.158	0.008	0.168
gene76	0.055	0.004	0.060
geneid.map	0.083	0.006	0.090
genius	0.254	0.010	0.283
ggi	0.095	0.004	0.106
ihc4	0.011	0.004	0.015
intrinsic.cluster	0.343	0.009	0.348
intrinsic.cluster.predict	0.207	0.004	0.214
map.datasets	0.881	0.015	0.915
mod1	0.002	0.000	0.003
mod2	0.002	0.001	0.003
modelOvcAngiogenic	0.002	0.001	0.003
molecular.subtyping	4.105	0.130	4.597
nkis	0.002	0.001	0.004
npi	0.007	0.003	0.011
oncotypedx	0.081	0.008	0.103
ovcAngiogenic	0.098	0.007	0.113
ovcCrijns	0.074	0.006	0.080
ovcTCGA	0.377	0.008	0.395
ovcYoshihara	0.072	0.003	0.077
pam50	0.027	0.003	0.032
pik3cags	0.086	0.008	0.094
power.cor	0.000	0.000	0.001
ps.cluster	0.664	0.015	0.663
read.m.file	0.048	0.002	0.049
rename.duplicate	0.003	0.000	0.003
rescale	0.029	0.004	0.033
rorS	0.426	0.012	0.442
scmgene.robust	0.007	0.001	0.008
scmod1.robust	0.008	0.001	0.009
scmod2.robust	0.008	0.002	0.009
setcolclass.df	0.003	0.000	0.003
sig.endoPredict	0.005	0.002	0.007
sig.gene70	0.007	0.002	0.011
sig.gene76	0.009	0.001	0.012
sig.genius	0.040	0.007	0.057
sig.ggi	0.008	0.001	0.009
sig.oncotypedx	0.005	0.002	0.007
sig.pik3cags	0.005	0.001	0.010
sig.score	0.086	0.004	0.110
sig.tamr13	0.007	0.003	0.010
sigOvcAngiogenic	0.009	0.002	0.012
sigOvcCrijns	0.009	0.002	0.011
sigOvcSpentzos	0.009	0.002	0.011
sigOvcTCGA	0.010	0.002	0.012
sigOvcYoshihara	0.009	0.001	0.011
spearmanCI	0.001	0.000	0.001
ssp2003	0.036	0.003	0.044
ssp2006	0.037	0.003	0.044
st.gallen	0.012	0.004	0.037
stab.fs	0.216	0.009	0.229
stab.fs.ranking	1.326	0.040	1.380
strescR	0.001	0.000	0.002
subtype.cluster	0.489	0.035	0.548
subtype.cluster.predict	0.171	0.016	0.188
tamr13	0.063	0.004	0.069
tbrm	0.001	0.000	0.001
vdxs	0.003	0.001	0.004
weighted.meanvar	0.001	0.000	0.001
write.m.file	0.003	0.001	0.004