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CHECK report for genefu on tokay1

This page was generated on 2019-04-13 11:21:36 -0400 (Sat, 13 Apr 2019).

Package 596/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.14.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK 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: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genefu.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings genefu_2.14.0.tar.gz
StartedAt: 2019-04-13 02:27:43 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:32:37 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 293.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: genefu.Rcheck
Warnings: 6

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genefu.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings genefu_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/genefu.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'genefu' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/expos.Rd:23: file link 'data.expos' in package 'genefu' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/nkis.Rd:23: file link 'data.nkis' in package 'genefu' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/read.m.file.Rd:16: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/vdxs.Rd:23: file link 'data.vdxs' in package 'genefu' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/write.m.file.Rd:22: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/genefu.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 6 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/genefu.Rcheck/00check.log'
for details.



Installation output

genefu.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/genefu_2.14.0.tar.gz && rm -rf genefu.buildbin-libdir && mkdir genefu.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genefu.buildbin-libdir genefu_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL genefu_2.14.0.zip && rm genefu_2.14.0.tar.gz genefu_2.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4324k  100 4324k    0     0  10.2M      0 --:--:-- --:--:-- --:--:-- 10.3M

install for i386

* installing *source* package 'genefu' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'genefu'
    finding HTML links ... done
    bimod                                   html  
    boxplotplus2                            html  
    claudinLow                              html  
    claudinLowData                          html  
    collapseIDs                             html  
    compare.proto.cor                       html  
    compute.pairw.cor.meta                  html  
    compute.pairw.cor.z                     html  
    compute.proto.cor.meta                  html  
    cordiff.dep                             html  
    endoPredict                             html  
    expos                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/expos.Rd:23: file link 'data.expos' in package 'genefu' does not exist and so has been treated as a topic
    fuzzy.ttest                             html  
    gene70                                  html  
    gene76                                  html  
    genefu-package                          html  
    geneid.map                              html  
    genius                                  html  
    ggi                                     html  
    ihc4                                    html  
    intrinsic.cluster                       html  
    intrinsic.cluster.predict               html  
    map.datasets                            html  
    medianCtr                               html  
    mod1                                    html  
    mod2                                    html  
    modelOvcAngiogenic                      html  
    molecular.subtyping                     html  
    nkis                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/nkis.Rd:23: file link 'data.nkis' in package 'genefu' does not exist and so has been treated as a topic
    npi                                     html  
    oncotypedx                              html  
    ovcAngiogenic                           html  
    ovcCrijns                               html  
    ovcTCGA                                 html  
    ovcYoshihara                            html  
    overlapSets                             html  
    pam50                                   html  
    pik3cags                                html  
    power.cor                               html  
    ps.cluster                              html  
    read.m.file                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/read.m.file.Rd:16: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
    readArray                               html  
    rename.duplicate                        html  
    rescale                                 html  
    rorS                                    html  
    scmgene.robust                          html  
    scmod1.robust                           html  
    scmod2.robust                           html  
    setcolclass.df                          html  
    sig.endoPredict                         html  
    sig.gene70                              html  
    sig.gene76                              html  
    sig.genius                              html  
    sig.ggi                                 html  
    sig.oncotypedx                          html  
    sig.pik3cags                            html  
    sig.score                               html  
    sig.tamr13                              html  
    sigOvcAngiogenic                        html  
    sigOvcCrijns                            html  
    sigOvcSpentzos                          html  
    sigOvcTCGA                              html  
    sigOvcYoshihara                         html  
    spearmanCI                              html  
    ssp2003                                 html  
    ssp2006                                 html  
    st.gallen                               html  
    stab.fs                                 html  
    stab.fs.ranking                         html  
    strescR                                 html  
    subtype.cluster                         html  
    subtype.cluster.predict                 html  
    tamr13                                  html  
    tbrm                                    html  
    vdxs                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/vdxs.Rd:23: file link 'data.vdxs' in package 'genefu' does not exist and so has been treated as a topic
    weighted.meanvar                        html  
    write.m.file                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/write.m.file.Rd:22: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'genefu' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genefu' as genefu_2.14.0.zip
* DONE (genefu)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'genefu' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

genefu.Rcheck/examples_i386/genefu-Ex.timings

nameusersystemelapsed
bimod0.220.010.24
boxplotplus2000
claudinLow0.820.000.81
claudinLowData0.120.080.21
compare.proto.cor0.830.000.83
compute.pairw.cor.meta0.940.161.09
compute.proto.cor.meta0.610.000.61
cordiff.dep0.030.000.03
endoPredict0.010.000.02
expos0.000.010.01
fuzzy.ttest000
gene700.100.020.11
gene760.030.020.05
geneid.map0.060.010.08
genius0.130.020.14
ggi0.040.010.06
ihc40.000.020.01
intrinsic.cluster0.210.000.21
intrinsic.cluster.predict0.110.010.12
map.datasets0.570.020.60
mod1000
mod2000
modelOvcAngiogenic0.000.000.01
molecular.subtyping1.820.082.75
nkis0.000.010.02
npi000
oncotypedx0.310.020.33
ovcAngiogenic0.060.000.06
ovcCrijns0.060.000.06
ovcTCGA0.180.010.19
ovcYoshihara0.040.000.05
pam500.020.020.03
pik3cags0.040.010.06
power.cor000
ps.cluster0.30.00.3
read.m.file0.020.000.11
rename.duplicate000
rescale0.030.020.05
rorS0.120.000.12
scmgene.robust0.020.000.02
scmod1.robust000
scmod2.robust0.000.010.01
setcolclass.df000
sig.endoPredict0.000.000.02
sig.gene70000
sig.gene760.000.020.02
sig.genius0.010.000.01
sig.ggi0.000.010.02
sig.oncotypedx0.020.000.01
sig.pik3cags000
sig.score0.060.020.08
sig.tamr13000
sigOvcAngiogenic0.000.020.02
sigOvcCrijns0.020.000.01
sigOvcSpentzos000
sigOvcTCGA0.000.010.02
sigOvcYoshihara000
spearmanCI000
ssp20030.030.000.03
ssp20060.060.010.08
st.gallen0.020.000.02
stab.fs0.110.000.11
stab.fs.ranking0.530.030.56
strescR000
subtype.cluster0.420.050.48
subtype.cluster.predict0.110.000.11
tamr130.050.000.05
tbrm000
vdxs000
weighted.meanvar000
write.m.file0.000.020.02

genefu.Rcheck/examples_x64/genefu-Ex.timings

nameusersystemelapsed
bimod0.230.000.23
boxplotplus20.000.020.02
claudinLow0.980.000.99
claudinLowData0.100.080.17
compare.proto.cor0.780.040.83
compute.pairw.cor.meta1.190.051.23
compute.proto.cor.meta0.720.020.74
cordiff.dep0.010.000.01
endoPredict0.020.010.03
expos0.000.020.02
fuzzy.ttest000
gene700.090.030.12
gene760.030.010.05
geneid.map0.050.020.06
genius0.120.030.16
ggi0.050.000.05
ihc40.000.020.01
intrinsic.cluster0.190.030.22
intrinsic.cluster.predict0.120.010.14
map.datasets0.720.020.74
mod1000
mod2000
modelOvcAngiogenic0.000.010.01
molecular.subtyping2.050.102.14
nkis0.000.010.02
npi000
oncotypedx0.050.020.06
ovcAngiogenic0.030.030.06
ovcCrijns0.040.020.07
ovcTCGA0.210.000.20
ovcYoshihara0.040.010.06
pam500.040.000.03
pik3cags0.050.000.05
power.cor000
ps.cluster0.290.020.31
read.m.file0.020.000.01
rename.duplicate000
rescale0.030.010.05
rorS0.110.020.13
scmgene.robust0.000.010.01
scmod1.robust000
scmod2.robust000
setcolclass.df000
sig.endoPredict0.000.020.01
sig.gene700.020.000.02
sig.gene76000
sig.genius0.010.000.01
sig.ggi0.000.010.02
sig.oncotypedx0.020.000.01
sig.pik3cags000
sig.score0.080.000.08
sig.tamr13000
sigOvcAngiogenic0.000.020.02
sigOvcCrijns000
sigOvcSpentzos0.000.010.01
sigOvcTCGA0.010.000.02
sigOvcYoshihara000
spearmanCI000
ssp20030.030.020.05
ssp20060.030.030.06
st.gallen0.000.020.01
stab.fs0.110.000.11
stab.fs.ranking0.630.010.64
strescR000
subtype.cluster0.390.030.43
subtype.cluster.predict0.090.020.11
tamr130.050.000.04
tbrm000
vdxs000
weighted.meanvar000
write.m.file0.000.010.02