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CHECK report for coGPS on tokay2

This page was generated on 2019-10-16 12:26:17 -0400 (Wed, 16 Oct 2019).

Package 322/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coGPS 1.28.0
Yingying Wei
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/coGPS
Branch: RELEASE_3_9
Last Commit: 94cfa1d
Last Changed Date: 2019-05-02 11:53:35 -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: coGPS
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coGPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings coGPS_1.28.0.tar.gz
StartedAt: 2019-10-16 02:49:36 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:50:20 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 44.5 seconds
RetCode: 0
Status:  OK  
CheckDir: coGPS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coGPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings coGPS_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/coGPS.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 'coGPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coGPS' version '1.28.0'
* 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 'coGPS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
PlotTopPCOPA: no visible global function definition for 'plot.new'
plotCOPA: no visible global function definition for 'barplot'
Undefined global functions or variables:
  barplot plot.new
Consider adding
  importFrom("graphics", "barplot", "plot.new")
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 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/coGPS.Rcheck/00check.log'
for details.



Installation output

coGPS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/coGPS_1.28.0.tar.gz && rm -rf coGPS.buildbin-libdir && mkdir coGPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=coGPS.buildbin-libdir coGPS_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL coGPS_1.28.0.zip && rm coGPS_1.28.0.tar.gz coGPS_1.28.0.zip
###
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  % 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 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100 1499k  100 1499k    0     0   530k      0  0:00:02  0:00:02 --:--:--  533k

install for i386

* installing *source* package 'coGPS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'coGPS'
    finding HTML links ... done
    PCOPA                                   html  
    PatientSpecificGeneList                 html  
    PlotTopPCOPA                            html  
    SampleData                              html  
    coGPS-internal                          html  
    coGPS-package                           html  
    permCOPA                                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 'coGPS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coGPS' as coGPS_1.28.0.zip
* DONE (coGPS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'coGPS' successfully unpacked and MD5 sums checked

Tests output


Example timings

coGPS.Rcheck/examples_i386/coGPS-Ex.timings

nameusersystemelapsed
PCOPA1.800.041.84
PatientSpecificGeneList1.310.081.39
PlotTopPCOPA1.140.021.15
permCOPA2.430.032.46

coGPS.Rcheck/examples_x64/coGPS-Ex.timings

nameusersystemelapsed
PCOPA1.350.031.38
PatientSpecificGeneList1.560.001.56
PlotTopPCOPA1.290.051.33
permCOPA3.480.033.51