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This page was generated on 2021-10-23 14:06:27 -0400 (Sat, 23 Oct 2021).

CHECK results for genefu on riesling1

To the developers/maintainers of the genefu package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genefu.git to
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raw results

Package 723/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.25.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/genefu
git_branch: master
git_last_commit: 8fce049
git_last_commit_date: 2021-05-21 19:08:16 -0400 (Fri, 21 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: genefu
Version: 2.25.1
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genefu.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings genefu_2.25.1.tar.gz
StartedAt: 2021-10-23 06:17:41 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 06:22:05 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 264.3 seconds
RetCode: 0
Status:   OK  
CheckDir: genefu.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genefu.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings genefu_2.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/genefu.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '2.25.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
* 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
Packages in Depends field not imported from:
  'AIMS' 'biomaRt' 'iC10'
  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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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
** 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/genefu.Rcheck/00check.log'
for details.



Installation output

genefu.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/genefu_2.25.1.tar.gz && rm -rf genefu.buildbin-libdir && mkdir genefu.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genefu.buildbin-libdir genefu_2.25.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL genefu_2.25.1.zip && rm genefu_2.25.1.tar.gz genefu_2.25.1.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
 65 4962k   65 3227k    0     0  4164k      0  0:00:01 --:--:--  0:00:01 4158k
100 4962k  100 4962k    0     0  4637k      0  0:00:01  0:00:01 --:--:-- 4641k

install for i386

* installing *source* package 'genefu' ...
** using staged installation
** R
** data
** 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  
    compareProtoCor                         html  
    compute.pairw.cor.meta                  html  
    compute.pairw.cor.z                     html  
    compute.proto.cor.meta                  html  
    cordiff.dep                             html  
    endoPredict                             html  
    expos                                   html  
    fuzzy.ttest                             html  
    gene70                                  html  
    gene76                                  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  
    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  
    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  
    weighted.meanvar                        html  
    write.m.file                            html  
** 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_2.25.1.zip
* DONE (genefu)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'genefu' successfully unpacked and MD5 sums checked

Tests output


Example timings

genefu.Rcheck/examples_i386/genefu-Ex.timings

nameusersystemelapsed
bimod0.220.020.24
boxplotplus2000
claudinLow0.390.010.41
compareProtoCor0.870.020.89
compute.pairw.cor.meta0.970.051.02
compute.proto.cor.meta0.800.010.81
cordiff.dep0.090.000.09
endoPredict0.130.000.13
fuzzy.ttest0.070.000.08
gene700.240.000.23
gene760.090.020.11
geneid.map0.100.030.12
genius0.150.030.19
ggi0.110.000.11
ihc40.10.00.1
intrinsic.cluster0.310.020.32
intrinsic.cluster.predict0.120.010.14
map.datasets0.800.020.82
molecular.subtyping1.690.041.79
npi0.090.000.10
oncotypedx0.110.000.11
ovcAngiogenic0.090.040.13
ovcCrijns0.090.000.09
ovcTCGA0.170.000.17
ovcYoshihara0.090.010.11
pik3cags0.100.020.11
power.cor000
ps.cluster0.250.010.26
read.m.file0.010.000.02
rename.duplicate000
rescale0.210.000.20
rorS0.130.020.14
setcolclass.df000
sig.score0.110.000.11
spearmanCI000
st.gallen0.090.000.09
stab.fs0.060.000.06
stab.fs.ranking0.30.00.3
strescR000
subtype.cluster0.610.020.62
subtype.cluster.predict0.230.020.25
tamr130.130.000.13
tbrm000
weighted.meanvar000
write.m.file0.000.010.01

genefu.Rcheck/examples_x64/genefu-Ex.timings

nameusersystemelapsed
bimod0.190.020.20
boxplotplus20.020.000.01
claudinLow0.420.000.42
compareProtoCor0.910.050.96
compute.pairw.cor.meta1.340.011.35
compute.proto.cor.meta0.820.050.86
cordiff.dep0.070.010.10
endoPredict0.080.000.08
fuzzy.ttest0.080.000.07
gene700.170.020.19
gene760.100.020.11
geneid.map0.090.000.09
genius0.160.010.18
ggi0.070.020.09
ihc40.080.000.07
intrinsic.cluster0.250.000.25
intrinsic.cluster.predict0.140.010.16
map.datasets0.860.000.86
molecular.subtyping1.340.061.41
npi0.080.000.07
oncotypedx0.090.020.11
ovcAngiogenic0.080.020.10
ovcCrijns0.100.010.11
ovcTCGA0.150.030.18
ovcYoshihara0.100.020.11
pik3cags0.090.000.10
power.cor000
ps.cluster0.270.000.26
read.m.file0.010.000.02
rename.duplicate000
rescale0.170.010.19
rorS0.130.020.14
setcolclass.df000
sig.score0.090.020.11
spearmanCI000
st.gallen0.080.000.07
stab.fs0.410.000.41
stab.fs.ranking0.320.000.33
strescR000
subtype.cluster0.490.040.53
subtype.cluster.predict0.170.030.20
tamr130.110.000.11
tbrm000
weighted.meanvar000
write.m.file000