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CHECK report for genefu on malbec1

This page was generated on 2019-04-16 11:49:08 -0400 (Tue, 16 Apr 2019).

Package 596/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.14.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/genefu
Branch: RELEASE_3_8
Last Commit: 0825dec
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: genefu
Version: 2.14.0
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

Command output

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### Running 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
###
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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.



Installation output

genefu.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output


Example timings

genefu.Rcheck/genefu-Ex.timings

nameusersystemelapsed
bimod0.2760.0080.284
boxplotplus20.0080.0000.011
claudinLow1.3880.0001.405
claudinLowData0.0880.0680.158
compare.proto.cor0.9400.0120.955
compute.pairw.cor.meta1.6280.0321.662
compute.proto.cor.meta0.8160.0000.816
cordiff.dep0.0120.0000.012
endoPredict0.0120.0040.015
expos0.0040.0000.002
fuzzy.ttest0.0000.0000.001
gene700.1160.0040.117
gene760.0200.0040.027
geneid.map0.0520.0000.055
genius0.1320.0040.139
ggi0.0480.0040.053
ihc40.0040.0000.006
intrinsic.cluster0.2880.0000.274
intrinsic.cluster.predict0.1760.0080.183
map.datasets0.8600.0080.869
mod10.0000.0000.002
mod20.0000.0000.002
modelOvcAngiogenic0.0000.0040.003
molecular.subtyping3.2560.0323.407
nkis0.4120.0000.410
npi0.0080.0000.006
oncotypedx0.0800.0000.081
ovcAngiogenic0.0760.0040.080
ovcCrijns0.0760.0040.078
ovcTCGA0.3400.0040.343
ovcYoshihara0.0720.0000.073
pam500.0280.0000.028
pik3cags0.0680.0080.074
power.cor000
ps.cluster0.4320.0040.413
read.m.file0.0200.0000.031
rename.duplicate0.0000.0000.001
rescale0.0480.0040.049
rorS0.0960.0000.097
scmgene.robust0.0000.0040.004
scmod1.robust0.0080.0000.005
scmod2.robust0.0040.0000.005
setcolclass.df0.0000.0040.001
sig.endoPredict0.0000.0000.003
sig.gene700.0040.0000.004
sig.gene760.0040.0000.004
sig.genius0.0120.0040.018
sig.ggi0.0040.0000.004
sig.oncotypedx0.0000.0000.003
sig.pik3cags0.0000.0000.004
sig.score0.0640.0080.072
sig.tamr130.0040.0000.004
sigOvcAngiogenic0.0040.0000.005
sigOvcCrijns0.0000.0040.004
sigOvcSpentzos0.0040.0000.004
sigOvcTCGA0.0080.0000.005
sigOvcYoshihara0.0000.0040.004
spearmanCI000
ssp20030.0240.0000.024
ssp20060.0280.0040.030
st.gallen0.0040.0000.006
stab.fs0.080.000.08
stab.fs.ranking0.6560.0080.664
strescR0.0000.0000.001
subtype.cluster0.40.00.4
subtype.cluster.predict0.1440.0040.147
tamr130.0400.0040.044
tbrm0.0000.0000.001
vdxs0.0040.0000.002
weighted.meanvar000
write.m.file0.0040.0000.003