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CHECK report for conumee on malbec1

This page was generated on 2019-04-16 11:51:16 -0400 (Tue, 16 Apr 2019).

Package 323/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.16.0
Volker Hovestadt
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/conumee
Branch: RELEASE_3_8
Last Commit: 4720c4a
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: conumee
Version: 1.16.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings conumee_1.16.0.tar.gz
StartedAt: 2019-04-15 23:09:13 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:45:04 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 2151.0 seconds
RetCode: 0
Status:  OK 
CheckDir: conumee.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings conumee_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/conumee.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ 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 ... 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNV.detailplot      109.112  0.460 109.725
CNV.genomeplot      100.184  0.616 101.007
CNV.detailplot_wrap  97.716  0.512  98.419
CNV.analysis-class   97.276  0.864  98.782
CNV.write            94.460  0.568  95.219
CNV.segment          78.764  0.132  78.995
CNV.fit              62.568  0.152  62.867
CNV.bin              55.308  0.168  55.574
CNV.detail           53.800  0.148  54.083
CNV.create_anno      49.240  0.000  49.365
CNV.anno-class       43.828  0.012  44.230
read.450k.url         8.692  0.220  17.826
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/conumee.Rcheck/00check.log’
for details.



Installation output

conumee.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL conumee
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘conumee’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (conumee)

Tests output


Example timings

conumee.Rcheck/conumee-Ex.timings

nameusersystemelapsed
CNV.analysis-class97.276 0.86498.782
CNV.anno-class43.828 0.01244.230
CNV.bin55.308 0.16855.574
CNV.create_anno49.240 0.00049.365
CNV.data-class3.9520.0724.066
CNV.detail53.800 0.14854.083
CNV.detailplot109.112 0.460109.725
CNV.detailplot_wrap97.716 0.51298.419
CNV.fit62.568 0.15262.867
CNV.genomeplot100.184 0.616101.007
CNV.load3.0000.0803.084
CNV.segment78.764 0.13278.995
CNV.write94.460 0.56895.219
read.450k.url 8.692 0.22017.826