Package: genefu

Version: 2.14.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings genefu_2.14.0.tar.gz

StartedAt: 2019-04-16 00:07:29 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:16:12 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 523.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genefu.Rcheck

Warnings: 5

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings genefu_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/genefu.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘2.14.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  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
Unknown packages ‘claudinLow’, ‘multilevel’, ‘dplR’ 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 files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/genefu.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL genefu
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘genefu’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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	0.276	0.008	0.284
boxplotplus2	0.008	0.000	0.011
claudinLow	1.388	0.000	1.405
claudinLowData	0.088	0.068	0.158
compare.proto.cor	0.940	0.012	0.955
compute.pairw.cor.meta	1.628	0.032	1.662
compute.proto.cor.meta	0.816	0.000	0.816
cordiff.dep	0.012	0.000	0.012
endoPredict	0.012	0.004	0.015
expos	0.004	0.000	0.002
fuzzy.ttest	0.000	0.000	0.001
gene70	0.116	0.004	0.117
gene76	0.020	0.004	0.027
geneid.map	0.052	0.000	0.055
genius	0.132	0.004	0.139
ggi	0.048	0.004	0.053
ihc4	0.004	0.000	0.006
intrinsic.cluster	0.288	0.000	0.274
intrinsic.cluster.predict	0.176	0.008	0.183
map.datasets	0.860	0.008	0.869
mod1	0.000	0.000	0.002
mod2	0.000	0.000	0.002
modelOvcAngiogenic	0.000	0.004	0.003
molecular.subtyping	3.256	0.032	3.407
nkis	0.412	0.000	0.410
npi	0.008	0.000	0.006
oncotypedx	0.080	0.000	0.081
ovcAngiogenic	0.076	0.004	0.080
ovcCrijns	0.076	0.004	0.078
ovcTCGA	0.340	0.004	0.343
ovcYoshihara	0.072	0.000	0.073
pam50	0.028	0.000	0.028
pik3cags	0.068	0.008	0.074
power.cor	0	0	0
ps.cluster	0.432	0.004	0.413
read.m.file	0.020	0.000	0.031
rename.duplicate	0.000	0.000	0.001
rescale	0.048	0.004	0.049
rorS	0.096	0.000	0.097
scmgene.robust	0.000	0.004	0.004
scmod1.robust	0.008	0.000	0.005
scmod2.robust	0.004	0.000	0.005
setcolclass.df	0.000	0.004	0.001
sig.endoPredict	0.000	0.000	0.003
sig.gene70	0.004	0.000	0.004
sig.gene76	0.004	0.000	0.004
sig.genius	0.012	0.004	0.018
sig.ggi	0.004	0.000	0.004
sig.oncotypedx	0.000	0.000	0.003
sig.pik3cags	0.000	0.000	0.004
sig.score	0.064	0.008	0.072
sig.tamr13	0.004	0.000	0.004
sigOvcAngiogenic	0.004	0.000	0.005
sigOvcCrijns	0.000	0.004	0.004
sigOvcSpentzos	0.004	0.000	0.004
sigOvcTCGA	0.008	0.000	0.005
sigOvcYoshihara	0.000	0.004	0.004
spearmanCI	0	0	0
ssp2003	0.024	0.000	0.024
ssp2006	0.028	0.004	0.030
st.gallen	0.004	0.000	0.006
stab.fs	0.08	0.00	0.08
stab.fs.ranking	0.656	0.008	0.664
strescR	0.000	0.000	0.001
subtype.cluster	0.4	0.0	0.4
subtype.cluster.predict	0.144	0.004	0.147
tamr13	0.040	0.004	0.044
tbrm	0.000	0.000	0.001
vdxs	0.004	0.000	0.002
weighted.meanvar	0	0	0
write.m.file	0.004	0.000	0.003