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CHECK report for genefu on tokay1

This page was generated on 2020-04-15 12:19:49 -0400 (Wed, 15 Apr 2020).

Package 653/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.18.1
Benjamin Haibe-Kains
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/genefu
Branch: RELEASE_3_10
Last Commit: 41b962e
Last Changed Date: 2020-01-31 16:18:01 -0400 (Fri, 31 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK 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  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genefu
Version: 2.18.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genefu.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings genefu_2.18.1.tar.gz
StartedAt: 2020-04-15 03:22:59 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:26:34 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 214.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: genefu.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genefu.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings genefu_2.18.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/genefu.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '2.18.1'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/genefu/man/cordiff.dep.Rd:53: file link 'compareProtoCor' in package 'genefu' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-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 ... NOTE
Unexported objects imported by ':::' calls:
  'mclust:::grid1' 'mclust:::grid2'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
claudinLow: no visible global function definition for 'standardize'
Undefined global functions or variables:
  standardize
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'multilevel'
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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
Examples with CPU or elapsed time > 5s
                    user system elapsed
molecular.subtyping 2.77   0.06    5.16
** 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: 1 WARNING, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-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/3.10/bioc/src/contrib/genefu_2.18.1.tar.gz && rm -rf genefu.buildbin-libdir && mkdir genefu.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genefu.buildbin-libdir genefu_2.18.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL genefu_2.18.1.zip && rm genefu_2.18.1.tar.gz genefu_2.18.1.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 4327k  100 4327k    0     0  14.2M      0 --:--:-- --:--:-- --:--:-- 14.4M

install for i386

* installing *source* package 'genefu' ...
** using staged installation
** 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  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/genefu/man/cordiff.dep.Rd:53: file link 'compareProtoCor' in package 'genefu' does not exist and so has been treated as a topic
    endoPredict                             html  
    expos                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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-3.10-bioc/tmpdir/RtmpgZcUvJ/R.INSTALL1de82acc54c6/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'genefu' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genefu' as genefu_2.18.1.zip
* DONE (genefu)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'genefu' successfully unpacked and MD5 sums checked

Tests output


Example timings

genefu.Rcheck/examples_i386/genefu-Ex.timings

nameusersystemelapsed
bimod0.330.020.35
boxplotplus20.020.000.01
claudinLow1.280.031.31
claudinLowData0.070.000.06
compare.proto.cor0.900.010.93
compute.pairw.cor.meta1.210.071.26
compute.proto.cor.meta0.760.010.78
cordiff.dep0.020.000.02
endoPredict0.030.000.03
expos000
fuzzy.ttest000
gene700.130.000.13
gene760.020.020.03
geneid.map0.070.010.09
genius0.200.030.23
ggi0.10.00.1
ihc40.000.020.01
intrinsic.cluster0.230.030.27
intrinsic.cluster.predict0.090.020.11
map.datasets0.850.010.86
mod10.010.000.01
mod2000
modelOvcAngiogenic0.000.020.02
molecular.subtyping2.770.065.16
nkis0.000.020.01
npi0.000.010.02
oncotypedx0.060.020.08
ovcAngiogenic0.050.010.06
ovcCrijns0.080.020.09
ovcTCGA0.180.000.19
ovcYoshihara0.070.000.06
pam500.010.010.03
pik3cags0.10.00.1
power.cor000
ps.cluster0.290.000.29
read.m.file0.030.000.07
rename.duplicate000
rescale0.040.020.04
rorS0.140.000.14
scmgene.robust0.000.010.02
scmod1.robust0.010.000.01
scmod2.robust000
setcolclass.df0.020.000.02
sig.endoPredict000
sig.gene700.010.000.02
sig.gene76000
sig.genius0.010.000.02
sig.ggi0.020.000.01
sig.oncotypedx0.000.020.02
sig.pik3cags0.000.020.01
sig.score0.090.000.10
sig.tamr130.020.000.01
sigOvcAngiogenic0.000.010.02
sigOvcCrijns0.010.000.01
sigOvcSpentzos000
sigOvcTCGA0.020.000.02
sigOvcYoshihara0.000.020.02
spearmanCI000
ssp20030.050.000.04
ssp20060.040.030.08
st.gallen000
stab.fs0.070.000.08
stab.fs.ranking0.610.110.72
strescR0.020.000.01
subtype.cluster0.670.030.71
subtype.cluster.predict0.170.000.17
tamr130.050.010.06
tbrm000
vdxs000
weighted.meanvar000
write.m.file0.010.000.01

genefu.Rcheck/examples_x64/genefu-Ex.timings

nameusersystemelapsed
bimod0.280.000.28
boxplotplus2000
claudinLow1.200.001.21
claudinLowData0.050.010.06
compare.proto.cor1.000.021.02
compute.pairw.cor.meta1.370.041.42
compute.proto.cor.meta0.900.030.92
cordiff.dep0.030.000.03
endoPredict0.030.020.05
expos000
fuzzy.ttest0.010.000.01
gene700.190.030.22
gene760.050.020.06
geneid.map0.120.000.13
genius0.240.030.27
ggi0.080.010.09
ihc40.010.000.01
intrinsic.cluster0.330.040.36
intrinsic.cluster.predict0.190.010.21
map.datasets0.950.020.97
mod1000
mod20.000.010.01
modelOvcAngiogenic000
molecular.subtyping2.590.052.64
nkis000
npi0.000.010.02
oncotypedx0.070.040.09
ovcAngiogenic0.070.030.11
ovcCrijns0.110.010.13
ovcTCGA0.280.020.29
ovcYoshihara0.080.010.10
pam500.030.040.06
pik3cags0.050.030.08
power.cor000
ps.cluster0.300.040.34
read.m.file0.020.000.01
rename.duplicate000
rescale0.030.020.05
rorS0.090.010.11
scmgene.robust0.020.000.01
scmod1.robust000
scmod2.robust0.020.000.02
setcolclass.df0.000.020.02
sig.endoPredict0.010.000.01
sig.gene700.000.020.02
sig.gene760.000.010.01
sig.genius0.020.020.03
sig.ggi0.000.010.02
sig.oncotypedx0.000.020.01
sig.pik3cags0.000.010.02
sig.score0.120.020.14
sig.tamr130.000.020.02
sigOvcAngiogenic0.020.000.01
sigOvcCrijns0.010.000.02
sigOvcSpentzos0.020.000.01
sigOvcTCGA0.010.000.02
sigOvcYoshihara0.000.010.01
spearmanCI000
ssp20030.070.000.07
ssp20060.040.020.06
st.gallen000
stab.fs0.110.000.10
stab.fs.ranking0.610.030.65
strescR000
subtype.cluster0.510.030.64
subtype.cluster.predict0.140.050.18
tamr130.080.000.08
tbrm000
vdxs000
weighted.meanvar000
write.m.file000