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CHECK report for CCPROMISE on tokay1

This page was generated on 2021-01-25 11:52:27 -0500 (Mon, 25 Jan 2021).

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 245/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CCPROMISE 1.16.0
Xueyuan Cao
Snapshot Date: 2021-01-24 14:40:16 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/CCPROMISE
Branch: RELEASE_3_12
Last Commit: f273cb2
Last Changed Date: 2020-10-27 11:19:17 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2021-01-25 01:19:19 -0500 (Mon, 25 Jan 2021)
EndedAt: 2021-01-25 01:23:48 -0500 (Mon, 25 Jan 2021)
EllapsedTime: 269.2 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_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CCPROMISE.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.16.0'
* 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         18.94   0.00   19.42
CCPROMISE-package 17.51   0.05   17.56
CANN              15.55   0.04   15.59
PrbPROMISE         8.25   0.06    8.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
CANN              18.62   0.00   18.62
CCPROMISE         15.60   0.01   15.61
CCPROMISE-package 14.75   0.05   14.79
PrbPROMISE         5.14   0.02    5.16
* 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
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_1.16.0.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_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CCPROMISE_1.16.0.zip && rm CCPROMISE_1.16.0.tar.gz CCPROMISE_1.16.0.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
100  976k  100  976k    0     0  2720k      0 --:--:-- --:--:-- --:--:-- 2750k

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_1.16.0.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
CANN15.55 0.0415.59
CCPROMISE-package17.51 0.0517.56
CCPROMISE18.94 0.0019.42
PROMISE21.360.021.37
PrbCor2.010.012.32
PrbPROMISE8.250.068.31

CCPROMISE.Rcheck/examples_x64/CCPROMISE-Ex.timings

nameusersystemelapsed
CANN18.62 0.0018.62
CCPROMISE-package14.75 0.0514.79
CCPROMISE15.60 0.0115.61
PROMISE21.010.021.03
PrbCor1.440.011.45
PrbPROMISE5.140.025.16