Back to Multiple platform build/check report for BioC 3.9
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for chroGPS on tokay2

This page was generated on 2019-10-16 12:27:06 -0400 (Wed, 16 Oct 2019).

Package 269/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 2.2.0
Oscar Reina
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/chroGPS
Branch: RELEASE_3_9
Last Commit: 77aa427
Last Changed Date: 2019-05-02 11:53:39 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chroGPS
Version: 2.2.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chroGPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings chroGPS_2.2.0.tar.gz
StartedAt: 2019-10-16 02:38:48 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:45:14 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 386.0 seconds
RetCode: 0
Status:  OK  
CheckDir: chroGPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chroGPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings chroGPS_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/chroGPS.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chroGPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chroGPS' version '2.2.0'
* 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 'chroGPS' can be installed ... OK
* 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 ... NOTE
chisqdist : : no visible global function definition for
  'RleList'
chisqdist :  : : no visible global function
  definition for 'Rle'
Undefined global functions or variables:
  Rle RleList
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
rankFactorsbyProfile 100.45   0.35   100.8
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
rankFactorsbyProfile 88.01   0.17   88.20
procrustesAdj         4.70   0.32    5.02
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'gtools'
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/chroGPS.Rcheck/00check.log'
for details.



Installation output

chroGPS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/chroGPS_2.2.0.tar.gz && rm -rf chroGPS.buildbin-libdir && mkdir chroGPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chroGPS.buildbin-libdir chroGPS_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL chroGPS_2.2.0.zip && rm chroGPS_2.2.0.tar.gz chroGPS_2.2.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3978k  100 3978k    0     0  41.1M      0 --:--:-- --:--:-- --:--:-- 43.6M

install for i386

* installing *source* package 'chroGPS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chroGPS'
    finding HTML links ... done
    addVar                                  html  
    adjustPeaks                             html  
    bg3                                     html  
    boostMDS                                html  
    clusGPS-class                           html  
    clusGPS                                 html  
    combineGenesMatrix                      html  
    diffFactors                             html  
    diffGenes                               html  
    distGPS-class                           html  
    distGPS                                 html  
    domainDist                              html  
    geneSetGPS                              html  
    getURL                                  html  
    gff2RDList                              html  
    gps2xgmml                               html  
    mds-class                               html  
    mds                                     html  
    mergeClusters                           html  
    mergeReplicates                         html  
    procrustesAdj                           html  
    profileClusters                         html  
    rankFactorsbyDomain                     html  
    rankFactorsbyProfile                    html  
    s2                                      html  
    splitDistGPS-class                      html  
** building package indices
** installing vignettes
   'chroGPS.Rnw' 
** 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 'chroGPS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chroGPS' as chroGPS_2.2.0.zip
* DONE (chroGPS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'chroGPS' successfully unpacked and MD5 sums checked

Tests output


Example timings

chroGPS.Rcheck/examples_i386/chroGPS-Ex.timings

nameusersystemelapsed
addVar000
adjustPeaks000
bg30.220.000.23
boostMDS000
clusGPS-class000
clusGPS000
combineGenesMatrix000
diffFactors0.480.030.51
diffGenes000
distGPS-class0.060.020.08
distGPS0.020.000.01
domainDist000
geneSetGPS000
getURL000
gff2RDList000
gps2xgmml000
mds-class000
mds000
mergeClusters000
mergeReplicates000
procrustesAdj3.780.274.04
profileClusters000
rankFactorsbyDomain0.080.010.10
rankFactorsbyProfile100.45 0.35100.80
s20.30.00.3
splitDistGPS-class000

chroGPS.Rcheck/examples_x64/chroGPS-Ex.timings

nameusersystemelapsed
addVar000
adjustPeaks000
bg30.310.000.31
boostMDS000
clusGPS-class000
clusGPS000
combineGenesMatrix000
diffFactors0.380.000.38
diffGenes000
distGPS-class0.100.000.11
distGPS0.020.000.02
domainDist000
geneSetGPS000
getURL000
gff2RDList000
gps2xgmml000
mds-class000
mds0.000.010.01
mergeClusters000
mergeReplicates000
procrustesAdj4.700.325.02
profileClusters000
rankFactorsbyDomain0.070.010.08
rankFactorsbyProfile88.01 0.1788.20
s20.240.000.23
splitDistGPS-class000