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CHECK report for CCPROMISE on tokay1

This page was generated on 2020-08-06 12:03:52 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CCPROMISE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 235/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CCPROMISE 1.15.0
Xueyuan Cao
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/CCPROMISE
Branch: master
Last Commit: eafda50
Last Changed Date: 2020-04-27 15:03:28 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CCPROMISE
Version: 1.15.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CCPROMISE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CCPROMISE_1.15.0.tar.gz
StartedAt: 2020-08-06 03:36:28 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 03:41:05 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 277.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CCPROMISE.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CCPROMISE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CCPROMISE_1.15.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CCPROMISE.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CCPROMISE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CCPROMISE' version '1.15.0'
* 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 'CCPROMISE' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CCPROMISE.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
CCPROMISE-package 20.07   0.13   20.19
CCPROMISE         19.93   0.06   20.00
CANN              18.82   0.20   19.05
PrbPROMISE         6.97   0.04    7.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
CCPROMISE         19.76   0.03   19.79
CCPROMISE-package 15.22   0.03   15.25
CANN              15.12   0.11   15.23
PrbPROMISE         5.63   0.01    5.64
* 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
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/CCPROMISE.Rcheck/00check.log'
for details.



Installation output

CCPROMISE.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CCPROMISE_1.15.0.tar.gz && rm -rf CCPROMISE.buildbin-libdir && mkdir CCPROMISE.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CCPROMISE.buildbin-libdir CCPROMISE_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CCPROMISE_1.15.0.zip && rm CCPROMISE_1.15.0.tar.gz CCPROMISE_1.15.0.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  976k  100  976k    0     0  17.4M      0 --:--:-- --:--:-- --:--:-- 18.6M

install for i386

* installing *source* package 'CCPROMISE' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
  converting help for package 'CCPROMISE'
    finding HTML links ... done
    CANN                                    html  
    CCPROMISE-package                       html  
    CCPROMISE                               html  
    PROMISE2                                html  
    PrbCor                                  html  
    PrbPROMISE                              html  
    exmplESet                               html  
    exmplGeneSet                            html  
    exmplMSet                               html  
    exmplPat                                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 'CCPROMISE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CCPROMISE' as CCPROMISE_1.15.0.zip
* DONE (CCPROMISE)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CCPROMISE' successfully unpacked and MD5 sums checked

Tests output


Example timings

CCPROMISE.Rcheck/examples_i386/CCPROMISE-Ex.timings

nameusersystemelapsed
CANN18.82 0.2019.05
CCPROMISE-package20.07 0.1320.19
CCPROMISE19.93 0.0620.00
PROMISE21.440.051.48
PrbCor2.020.002.02
PrbPROMISE6.970.047.01

CCPROMISE.Rcheck/examples_x64/CCPROMISE-Ex.timings

nameusersystemelapsed
CANN15.12 0.1115.23
CCPROMISE-package15.22 0.0315.25
CCPROMISE19.76 0.0319.79
PROMISE21.100.031.13
PrbCor1.230.021.25
PrbPROMISE5.630.015.64