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BioC 3.2: CHECK report for conumee on zin1

This page was generated on 2016-04-23 10:14:41 -0700 (Sat, 23 Apr 2016).

Package 219/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.2.0
Volker Hovestadt
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/conumee
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: conumee
Version: 1.2.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.2.0.tar.gz
StartedAt: 2016-04-22 23:32:09 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:49:20 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 1030.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: conumee.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/conumee.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.2.0’
* 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 ... [21s/21s] 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,matrix : .local: no visible binding for global variable ‘anno’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNV.data,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [14m/14m] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNV.detailplot_wrap 103.301  0.332 104.094
CNV.analysis-class   99.493  0.468  99.999
CNV.genomeplot       98.615  0.375  99.252
CNV.write            98.141  0.416  98.646
CNV.detailplot       94.832  0.348  95.245
CNV.segment          88.731  0.036  88.823
CNV.fit              49.740  0.020  49.822
CNV.detail           42.673  0.080  42.792
CNV.bin              41.735  0.076  41.817
CNV.anno-class       37.519  0.083  37.613
CNV.create_anno      36.964  0.007  36.996
read.450k.url         4.448  0.080  13.167
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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-class99.493 0.46899.999
CNV.anno-class37.519 0.08337.613
CNV.bin41.735 0.07641.817
CNV.create_anno36.964 0.00736.996
CNV.data-class1.5250.0161.542
CNV.detail42.673 0.08042.792
CNV.detailplot94.832 0.34895.245
CNV.detailplot_wrap103.301 0.332104.094
CNV.fit49.740 0.02049.822
CNV.genomeplot98.615 0.37599.252
CNV.load1.7620.0121.776
CNV.segment88.731 0.03688.823
CNV.write98.141 0.41698.646
read.450k.url 4.448 0.08013.167