Back to Multiple platform build/check report for BioC 3.6
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for conumee on tokay1

This page was generated on 2018-02-22 14:51:15 -0500 (Thu, 22 Feb 2018).

Package 289/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.12.0
Volker Hovestadt
Snapshot Date: 2018-02-21 17:00:20 -0500 (Wed, 21 Feb 2018)
URL: https://git.bioconductor.org/packages/conumee
Branch: RELEASE_3_6
Last Commit: fe49e1e
Last Changed Date: 2017-10-30 12:40:50 -0500 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: conumee
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.12.0.tar.gz
StartedAt: 2018-02-21 23:24:22 -0500 (Wed, 21 Feb 2018)
EndedAt: 2018-02-22 00:00:58 -0500 (Thu, 22 Feb 2018)
EllapsedTime: 2195.9 seconds
RetCode: 0
Status:  OK  
CheckDir: conumee.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/conumee.Rcheck'
* using R version 3.4.3 (2017-11-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'conumee/DESCRIPTION' ... OK
* this is package 'conumee' version '1.12.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'conumee' 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
* 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 loading without being on the library search path ... 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
CNV.load,GenomicRatioSet: no visible global function definition for
  'assays'
CNV.load,matrix: no visible binding for global variable 'anno'
Undefined global functions or variables:
  anno assays
* 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 R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
CNV.detailplot      107.33   1.41  108.73
CNV.detailplot_wrap 106.43   1.37  107.81
CNV.genomeplot       93.05   1.77   94.81
CNV.write            90.83   1.70   92.55
CNV.segment          86.16   1.08   87.23
CNV.analysis-class   79.50   1.37   80.89
CNV.fit              56.33   0.84   57.18
CNV.detail           45.13   0.39   45.52
CNV.create_anno      43.98   0.09   44.08
CNV.bin              41.97   0.53   42.50
CNV.anno-class       34.67   0.24   34.90
read.450k.url         8.00   0.85   18.51
* 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-3.6-bioc/meat/conumee.Rcheck/00check.log'
for details.



Installation output

conumee.Rcheck/00install.out

* installing *source* package 'conumee' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (conumee)
In R CMD INSTALL

Tests output


Example timings

conumee.Rcheck/conumee-Ex.timings

nameusersystemelapsed
CNV.analysis-class79.50 1.3780.89
CNV.anno-class34.67 0.2434.90
CNV.bin41.97 0.5342.50
CNV.create_anno43.98 0.0944.08
CNV.data-class3.110.163.26
CNV.detail45.13 0.3945.52
CNV.detailplot107.33 1.41108.73
CNV.detailplot_wrap106.43 1.37107.81
CNV.fit56.33 0.8457.18
CNV.genomeplot93.05 1.7794.81
CNV.load2.040.252.30
CNV.segment86.16 1.0887.23
CNV.write90.83 1.7092.55
read.450k.url 8.00 0.8518.51