Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for made4 on tokay1

This page was generated on 2021-05-06 12:32:06 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the made4 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 988/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.64.0  (landing page)
Aedin Culhane
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/made4
Branch: RELEASE_3_12
Last Commit: 89d0a81
Last Changed Date: 2020-10-27 10:25:28 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: made4
Version: 1.64.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:made4.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings made4_1.64.0.tar.gz
StartedAt: 2021-05-06 04:12:35 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:16:10 -0400 (Thu, 06 May 2021)
EllapsedTime: 214.8 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: made4.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:made4.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings made4_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/made4.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'made4/DESCRIPTION' ... OK
* this is package 'made4' version '1.64.0'
* 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 'made4' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/asDataFrame.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/asDataFrame.Rd:24: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bet.coinertia.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bet.coinertia.Rd:21: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.Rd:16: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.jackknife.Rd:37: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.suppl.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.suppl.Rd:19: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.suppl.Rd:45: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.suppl.Rd:63: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/cia.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/cia.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/heatplot.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/isDataFrame.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/isDataFrame.Rd:28: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/ord.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/overview.Rd:11: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/plotarrays.Rd:47: file link 's.groups' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/plotarrays.Rd:48: file link 's.match.col' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/prettyDend.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/s.var.Rd:65: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/s.var.Rd:65: file link 'plot.cia' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/suppl.Rd:18: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/suppl.Rd:39: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/suppl.Rd:48: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/made4.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 ... OK
* 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 ... NOTE
prepare_Rd: asDataFrame.Rd:30: Dropping empty section \examples
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/made4.Rcheck/00check.log'
for details.

Installation output

made4.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/made4_1.64.0.tar.gz && rm -rf made4.buildbin-libdir && mkdir made4.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=made4.buildbin-libdir made4_1.64.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL made4_1.64.0.zip && rm made4_1.64.0.tar.gz made4_1.64.0.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  700k  100  700k    0     0  2032k      0 --:--:-- --:--:-- --:--:-- 2036k

install for i386

* installing *source* package 'made4' ...
** 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 'made4'
    finding HTML links ... done
    NCI60                                   html  
    asDataFrame                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/asDataFrame.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/asDataFrame.Rd:24: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    bet.coinertia                           html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bet.coinertia.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bet.coinertia.Rd:21: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    between.graph                           html  
    bga                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.Rd:16: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    bga.jackknife                           html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.jackknife.Rd:37: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
    bga.suppl                               html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.suppl.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.suppl.Rd:19: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.suppl.Rd:45: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/bga.suppl.Rd:63: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
    checkfac                                html  
    chime3D                                 html  
    cia                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/cia.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/cia.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    commonMap                               html  
    comparelists                            html  
    do3d                                    html  
    dudi.rwcoa                              html  
    forrwcoa                                html  
    genes                                   html  
    genes1d                                 html  
    getcol                                  html  
    graph1D                                 html  
    heatplot                                html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/heatplot.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    html3D                                  html  
    isDataFrame                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/isDataFrame.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/isDataFrame.Rd:28: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    jmol3D                                  html  
    khan                                    html  
    ord                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/ord.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    overview                                html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/overview.Rd:11: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    plotarrays                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/plotarrays.Rd:47: file link 's.groups' in package 'made4' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/plotarrays.Rd:48: file link 's.match.col' in package 'made4' does not exist and so has been treated as a topic
    plotgenes                               html  
    prettyDend                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/prettyDend.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    randomiser                              html  
    s.var                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/s.var.Rd:65: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/s.var.Rd:65: file link 'plot.cia' in package 'made4' does not exist and so has been treated as a topic
    sumstats                                html  
    suppl                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/suppl.Rd:18: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/suppl.Rd:39: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpS0IHZQ/R.INSTALL1e346a70558e/made4/man/suppl.Rd:48: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
    topgenes                                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 'made4' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'made4' as made4_1.64.0.zip
* DONE (made4)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'made4' successfully unpacked and MD5 sums checked

Tests output

Example timings

made4.Rcheck/examples_i386/made4-Ex.timings

nameusersystemelapsed
NCI60000
bet.coinertia0.010.000.01
between.graph0.590.010.61
bga0.350.140.48
bga.jackknife1.370.211.58
bga.suppl0.390.030.42
cia0.180.030.20
commonMap0.030.000.04
comparelists000
do3d0.310.060.37
genes1d0.080.020.09
getcol0.030.000.04
graph1D0.080.000.07
heatplot1.970.052.02
html3D0.260.000.27
isDataFrame0.030.000.03
khan0.030.000.03
ord0.280.000.28
overview0.150.000.14
plotarrays0.250.000.25
plotgenes0.210.010.23
prettyDend0.140.020.16
randomiser000
s.var0.210.000.20
sumstats0.310.000.32
suppl0.410.010.42
topgenes0.060.020.08

made4.Rcheck/examples_x64/made4-Ex.timings

nameusersystemelapsed
NCI600.000.020.02
bet.coinertia0.020.000.01
between.graph0.730.000.73
bga0.340.030.38
bga.jackknife1.500.171.67
bga.suppl0.390.000.39
cia0.210.000.20
commonMap0.030.000.04
comparelists000
do3d0.400.020.41
genes1d0.090.000.09
getcol0.050.000.05
graph1D0.040.010.06
heatplot1.890.021.90
html3D0.760.010.88
isDataFrame0.040.000.03
khan0.000.020.01
ord0.260.000.27
overview0.130.000.13
plotarrays0.250.000.25
plotgenes0.120.000.12
prettyDend0.090.000.09
randomiser0.020.000.02
s.var0.220.000.21
sumstats0.180.000.19
suppl0.410.000.40
topgenes0.090.000.10