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BioC 3.5: CHECK report for genefu on veracruz2

This page was generated on 2017-10-18 14:29:26 -0400 (Wed, 18 Oct 2017).

Package 512/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.8.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/genefu
Branch: RELEASE_3_5
Last Commit: 83aae9f
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: genefu
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.8.0.tar.gz
StartedAt: 2017-10-18 03:57:43 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 04:00:29 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 166.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: genefu.Rcheck
Warnings: 5

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genefu.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.8.0’
* 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  6.5Mb
  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 ... 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-3.5-bioc/meat/genefu.Rcheck/00check.log’
for details.


genefu.Rcheck/00install.out:

* 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)

genefu.Rcheck/genefu-Ex.timings:

nameusersystemelapsed
bimod0.2360.0150.254
boxplotplus20.0100.0010.011
claudinLow1.2470.0311.308
claudinLowData0.1480.1430.298
compare.proto.cor1.1770.0261.238
compute.pairw.cor.meta1.2990.0301.370
compute.proto.cor.meta0.8030.0230.851
cordiff.dep0.0120.0030.016
endoPredict0.0180.0050.023
expos0.0030.0020.004
fuzzy.ttest0.0240.0000.026
gene700.2240.0090.239
gene760.0360.0030.042
geneid.map0.0690.0050.079
genius0.3260.0060.346
ggi0.0620.0050.068
ihc40.1130.0040.125
intrinsic.cluster0.2750.0080.272
intrinsic.cluster.predict0.3860.0050.403
map.datasets0.6390.0130.688
mod10.0010.0000.002
mod20.0030.0010.003
modelOvcAngiogenic0.0020.0020.004
molecular.subtyping4.1090.1274.365
nkis0.0020.0010.003
npi0.0050.0030.009
oncotypedx0.0700.0060.079
ovcAngiogenic0.0540.0070.063
ovcCrijns0.0630.0080.072
ovcTCGA0.2620.0050.272
ovcYoshihara0.0500.0040.056
pam500.0190.0030.023
pik3cags0.0590.0040.067
power.cor0.0010.0010.001
ps.cluster0.9530.0200.984
read.m.file0.0630.0020.068
rename.duplicate0.0020.0000.002
rescale0.0380.0030.044
rorS0.1380.0070.149
scmgene.robust0.0060.0010.007
scmod1.robust0.0060.0020.008
scmod2.robust0.0060.0010.008
setcolclass.df0.0020.0000.003
sig.endoPredict0.0040.0010.005
sig.gene700.0050.0010.006
sig.gene760.0060.0020.007
sig.genius0.0330.0080.042
sig.ggi0.0060.0010.009
sig.oncotypedx0.0040.0010.008
sig.pik3cags0.0030.0020.006
sig.score0.0810.0040.087
sig.tamr130.0060.0030.010
sigOvcAngiogenic0.0060.0010.008
sigOvcCrijns0.0070.0020.009
sigOvcSpentzos0.0070.0020.008
sigOvcTCGA0.0080.0020.010
sigOvcYoshihara0.0060.0020.008
spearmanCI0.0010.0000.002
ssp20030.0300.0040.034
ssp20060.0400.0040.046
st.gallen0.0090.0030.013
stab.fs0.1850.0040.196
stab.fs.ranking1.0250.0381.096
strescR0.0220.0010.022
subtype.cluster0.7040.0310.757
subtype.cluster.predict0.1150.0100.128
tamr130.0630.0110.074
tbrm0.0010.0000.001
vdxs0.0020.0010.003
weighted.meanvar0.0010.0010.000
write.m.file0.0030.0010.004