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BioC 3.5: CHECK report for conumee on veracruz2

This page was generated on 2017-10-18 14:33:11 -0400 (Wed, 18 Oct 2017).

Package 273/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.10.0
Volker Hovestadt
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/conumee
Branch: RELEASE_3_5
Last Commit: 968ae0d
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: conumee
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings conumee_1.10.0.tar.gz
StartedAt: 2017-10-18 02:08:25 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:45:15 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 2210.5 seconds
RetCode: 0
Status:  OK 
CheckDir: conumee.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings conumee_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/conumee.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ 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 ... 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 for sufficient/correct file permissions ... 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.genomeplot      106.948  4.505 114.547
CNV.detailplot      105.090  4.543 112.881
CNV.write           103.708  3.719 110.448
CNV.detailplot_wrap  98.334  3.921 105.642
CNV.analysis-class   82.482  3.749  89.088
CNV.segment          81.333  3.093  86.730
CNV.fit              62.785  2.492  67.312
CNV.detail           54.707  2.849  59.740
CNV.bin              52.121  2.579  56.788
CNV.anno-class       46.454  1.876  50.235
CNV.create_anno      45.700  2.262  49.670
CNV.load              7.632  0.811   8.681
read.450k.url         7.940  0.500  16.028
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/conumee.Rcheck/00check.log’
for details.


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)

conumee.Rcheck/conumee-Ex.timings:

nameusersystemelapsed
CNV.analysis-class82.482 3.74989.088
CNV.anno-class46.454 1.87650.235
CNV.bin52.121 2.57956.788
CNV.create_anno45.700 2.26249.670
CNV.data-class2.8220.3933.298
CNV.detail54.707 2.84959.740
CNV.detailplot105.090 4.543112.881
CNV.detailplot_wrap 98.334 3.921105.642
CNV.fit62.785 2.49267.312
CNV.genomeplot106.948 4.505114.547
CNV.load7.6320.8118.681
CNV.segment81.333 3.09386.730
CNV.write103.708 3.719110.448
read.450k.url 7.940 0.50016.028