Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:08 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cogena on tokay2


To the developers/maintainers of the cogena package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cogena.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 369/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cogena 1.28.0  (landing page)
Zhilong Jia
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/cogena
git_branch: RELEASE_3_14
git_last_commit: 639d8fb
git_last_commit_date: 2021-10-26 12:19:56 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: cogena
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cogena.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cogena_1.28.0.tar.gz
StartedAt: 2022-01-20 17:54:19 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:01:15 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 416.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cogena.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cogena.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cogena_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cogena.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cogena/DESCRIPTION' ... OK
* this is package 'cogena' version '1.28.0'
* 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 'cogena' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cogena.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.6Mb
* 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 ... NOTE
dist.fn: no visible global function definition for 'cor'
heatmap.3: no visible binding for global variable 'dist'
heatmap.3: no visible global function definition for 'par'
heatmap.3: no visible global function definition for 'median'
heatmap.3: no visible global function definition for 'order.dendrogram'
heatmap.3: no visible global function definition for 'reorder'
heatmap.3: no visible binding for global variable 'sd'
heatmap.3: no visible global function definition for 'layout'
heatmap.3: no visible global function definition for 'image'
heatmap.3: no visible global function definition for 'axis'
heatmap.3: no visible global function definition for 'mtext'
heatmap.3: no visible global function definition for 'rect'
heatmap.3: no visible global function definition for 'abline'
heatmap.3: no visible global function definition for 'lines'
heatmap.3: no visible global function definition for 'text'
heatmap.3: no visible global function definition for 'plot.new'
heatmap.3: no visible global function definition for 'title'
heatmap.3: no visible global function definition for 'density'
heatmap.3: no visible global function definition for 'hist'
plot.sota: no visible global function definition for 'par'
corInCluster,cogena: no visible global function definition for 'cor'
heatmapCluster,cogena: no visible global function definition for
  'topo.colors'
heatmapCluster,cogena: no visible global function definition for
  'rainbow'
heatmapCluster,cogena: no visible global function definition for 'par'
heatmapCluster,cogena: no visible global function definition for
  'legend'
heatmapPEI,cogena: no visible binding for global variable 'clusterID'
heatmapPEI,cogena: no visible binding for global variable 'TF'
heatmapPEI,cogena: no visible binding for global variable
  'clusterNumGene'
heatmapPEI,cogena: no visible binding for global variable 'GS'
heatmapPEI,cogena: no visible binding for global variable 'value'
heatmapPEI,cogena: no visible binding for global variable 'GeneCount'
Undefined global functions or variables:
  GS GeneCount TF abline axis clusterID clusterNumGene cor density dist
  hist image layout legend lines median mtext order.dendrogram par
  plot.new rainbow rect reorder sd text title topo.colors value
Consider adding
  importFrom("grDevices", "rainbow", "topo.colors")
  importFrom("graphics", "abline", "axis", "hist", "image", "layout",
             "legend", "lines", "mtext", "par", "plot.new", "rect",
             "text", "title")
  importFrom("stats", "cor", "density", "dist", "median",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
* 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 LazyData ... 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 (user + system) or elapsed time > 5s
               user system elapsed
cogena_package 6.41   0.86   86.46
clEnrich_one   3.68   0.11   12.33
upDownGene     2.78   0.18   17.06
clEnrich       2.69   0.12   16.61
clusterMethods 1.50   0.00   10.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
cogena_package 6.46   1.00   84.34
clEnrich_one   3.09   0.07   12.04
clEnrich       2.48   0.19   17.06
upDownGene     2.20   0.22   15.55
clusterMethods 1.16   0.02    9.16
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/cogena.Rcheck/00check.log'
for details.



Installation output

cogena.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cogena_1.28.0.tar.gz && rm -rf cogena.buildbin-libdir && mkdir cogena.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cogena.buildbin-libdir cogena_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cogena_1.28.0.zip && rm cogena_1.28.0.tar.gz cogena_1.28.0.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
 30 4588k   30 1379k    0     0  2354k      0  0:00:01 --:--:--  0:00:01 2353k
100 4588k  100 4588k    0     0  3308k      0  0:00:01  0:00:01 --:--:-- 3310k

install for i386

* installing *source* package 'cogena' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
** help
*** installing help indices
  converting help for package 'cogena'
    finding HTML links ... done
    AllGeneSymbols                          html  
    DEexprs                                 html  
    PEI                                     html  
    Psoriasis                               html  
    clEnrich                                html  
    clEnrich_one                            html  
    clusterMethods                          html  
    coExp                                   html  
    cogena_class                            html  
    cogena_package                          html  
    corInCluster                            html  
    enrichment                              html  
    gene2set                                html  
    geneExpInCluster                        html  
    geneInCluster                           html  
    genecl_class                            html  
    geneclusters                            html  
    gmt2list                                html  
    gmtlist2file                            html  
    heatmap.3                               html  
    heatmapCluster                          html  
    heatmapCmap                             html  
    heatmapPEI                              html  
    mat                                     html  
    nClusters                               html  
    pClusters                               html  
    sampleLabel                             html  
    show                                    html  
    sota                                    html  
    summary                                 html  
    upDownGene                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'cogena' ...
** testing if installed package can be loaded
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
* MD5 sums
packaged installation of 'cogena' as cogena_1.28.0.zip
* DONE (cogena)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cogena' successfully unpacked and MD5 sums checked

Tests output


Example timings

cogena.Rcheck/examples_i386/cogena-Ex.timings

nameusersystemelapsed
PEI0.620.080.74
clEnrich 2.69 0.1216.61
clEnrich_one 3.68 0.1112.33
clusterMethods 1.50 0.0010.95
coExp000
cogena_package 6.41 0.8686.46
corInCluster000
enrichment000
gene2set0.030.020.04
geneExpInCluster000
geneInCluster0.000.010.02
geneclusters000
gmt2list0.020.000.02
gmtlist2file0.040.030.07
heatmapCluster0.020.000.02
heatmapCmap000
heatmapPEI0.020.000.02
mat000
nClusters000
show000
sota1.340.001.34
summary000
upDownGene 2.78 0.1817.06

cogena.Rcheck/examples_x64/cogena-Ex.timings

nameusersystemelapsed
PEI0.660.020.67
clEnrich 2.48 0.1917.06
clEnrich_one 3.09 0.0712.04
clusterMethods1.160.029.16
coExp000
cogena_package 6.46 1.0084.34
corInCluster000
enrichment000
gene2set0.030.000.04
geneExpInCluster0.020.000.01
geneInCluster000
geneclusters000
gmt2list0.010.000.02
gmtlist2file0.080.000.08
heatmapCluster000
heatmapCmap000
heatmapPEI0.000.020.01
mat000
nClusters000
show000
sota1.520.011.53
summary000
upDownGene 2.20 0.2215.55