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BioC 2.12: CHECK report for FunciSNP on george2

This page was generated on 2013-10-09 09:37:53 -0700 (Wed, 09 Oct 2013).

Package 240/671HostnameOS / ArchBUILDCHECKBUILD BIN
FunciSNP 1.2.0
Simon G. Coetzee
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/FunciSNP
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: FunciSNP
Version: 1.2.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings FunciSNP_1.2.0.tar.gz
StartedAt: 2013-10-09 01:50:07 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:01:15 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 668.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: FunciSNP.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/FunciSNP.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FunciSNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FunciSNP’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FunciSNP’ can be installed ... [62s/63s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
AnnotateSummary: no visible binding for '<<-' assignment to ‘txdb’
AnnotateSummary: no visible binding for global variable ‘txdb’
FunciSNPplot: no visible binding for global variable ‘R.squared’
FunciSNPplot: no visible binding for global variable ‘r.2’
FunciSNPplot: no visible binding for global variable
  ‘distance.from.tag’
FunciSNPplot: no visible binding for global variable ‘variable’
FunciSNPplot: no visible binding for global variable ‘sig’
FunciSNPplot: no visible binding for global variable ‘value’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getFSNPs':
getFSNPs
  Code: function(snp.regions.file, bio.features.loc = NULL,
                 built.in.biofeatures = TRUE, par.threads =
                 detectCores()/2, verbose = par.threads < 2, method.p =
                 "BH", search.window = 2e+05, primary.server = "ebi")
  Docs: function(snp.regions.file, bio.features.loc = NULL,
                 built.in.biofeatures = TRUE, par.threads =
                 detectCores()/2, verbose = par.threads < 2, method.p =
                 "BH", search.window = 2e+05)
  Argument names in code not in docs:
    primary.server

* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
FunciSNP-package 7.057  0.108   7.176
FunciSNPtable    5.061  0.372   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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/FunciSNP.Rcheck/00check.log’
for details.

FunciSNP.Rcheck/00install.out:

* installing *source* package ‘FunciSNP’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FunciSNP)

FunciSNP.Rcheck/FunciSNP-Ex.timings:

nameusersystemelapsed
CorrelatedSNPs-class1.0600.0041.064
FunciSNP-package7.0570.1087.176
FunciSNPAnnotateSummary1.3880.1001.507
FunciSNPbed1.5120.0121.543
FunciSNPidsFromSummary0.0040.0000.005
FunciSNPplot4.4200.0684.504
FunciSNPsummaryOverlaps1.4680.0761.543
FunciSNPtable5.0610.3725.448
TSList-class0.0280.0000.028
TagSNP-class0.0360.0000.033
getFSNPs1.5000.1561.676