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CHECK report for CCPROMISE on malbec2

This page was generated on 2019-10-16 12:09:59 -0400 (Wed, 16 Oct 2019).

Package 221/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CCPROMISE 1.10.0
Xueyuan Cao
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CCPROMISE
Branch: RELEASE_3_9
Last Commit: 2ee6dd3
Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CCPROMISE
Version: 1.10.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CCPROMISE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CCPROMISE_1.10.0.tar.gz
StartedAt: 2019-10-16 00:19:20 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:22:16 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 176.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CCPROMISE.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CCPROMISE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CCPROMISE_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CCPROMISE.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CCPROMISE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CCPROMISE’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... 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 ‘/home/biocbuild/bbs-3.9-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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
CCPROMISE         21.431  0.112  21.669
CANN              21.357  0.056  21.890
CCPROMISE-package 18.896  0.028  19.173
PrbPROMISE         5.432  0.016   5.448
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CCPROMISE.Rcheck/00check.log’
for details.



Installation output

CCPROMISE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CCPROMISE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* 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
** 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
* DONE (CCPROMISE)

Tests output


Example timings

CCPROMISE.Rcheck/CCPROMISE-Ex.timings

nameusersystemelapsed
CANN21.357 0.05621.890
CCPROMISE-package18.896 0.02819.173
CCPROMISE21.431 0.11221.669
PROMISE21.0480.0001.183
PrbCor1.1860.0121.198
PrbPROMISE5.4320.0165.448