Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for subSeq on perceval

This page was generated on 2015-11-10 14:50:14 -0800 (Tue, 10 Nov 2015).

Package 1029/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
subSeq 1.0.1
Andrew J. Bass , John D. Storey
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/subSeq
Last Changed Rev: 109694 / Revision: 110496
Last Changed Date: 2015-10-16 11:08:47 -0700 (Fri, 16 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: subSeq
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings subSeq_1.0.1.tar.gz
StartedAt: 2015-11-10 09:58:33 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 10:01:55 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 201.4 seconds
RetCode: 0
Status:  OK 
CheckDir: subSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings subSeq_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/subSeq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘subSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘subSeq’ version ‘1.0.1’
* 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 ‘subSeq’ can be installed ... [4s/4s] 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
plot.summary.subsamples: no visible binding for global variable
  ‘metric’
plot.summary.subsamples: no visible binding for global variable ‘value’
plot.summary.subsamples: no visible binding for global variable
  ‘significant’
plot.summary.subsamples: no visible binding for global variable
  ‘percent’
plot.summary.subsamples: no visible binding for global variable
  ‘method’
plot.summary.subsamples: no visible binding for global variable ‘depth’
plot.summary.subsamples: no visible binding for global variable
  ‘average.depth’
plot.summary.subsamples: no visible binding for global variable
  ‘average.value’
subsample: no visible binding for global variable ‘proportion’
subsample: no visible binding for global variable ‘replication’
subsample: no visible binding for global variable ‘.’
subsample: no visible binding for global variable ‘pvalue’
summary.subsamples: no visible binding for global variable ‘count’
summary.subsamples: no visible binding for global variable ‘method’
summary.subsamples: no visible binding for global variable ‘depth’
summary.subsamples: no visible binding for global variable ‘pvalue’
summary.subsamples: no visible binding for global variable ‘proportion’
summary.subsamples: no visible binding for global variable
  ‘replication’
summary.subsamples: no visible binding for global variable ‘ID’
summary.subsamples: no visible binding for global variable ‘padj’
summary.subsamples: no visible binding for global variable
  ‘coefficient’
summary.subsamples: no visible binding for global variable
  ‘o.coefficient’
summary.subsamples: no visible binding for global variable ‘valid’
summary.subsamples: no visible binding for global variable ‘o.lfdr’
summary.subsamples: no visible binding for global variable ‘o.padj’
summary.subsamples: no visible binding for global variable
  ‘significant’
summary.subsamples: no visible binding for global variable ‘estFDP’
summary.subsamples: no visible binding for global variable ‘rFDP’
summary.subsamples: no visible binding for global variable ‘metric’
summary.subsamples: no visible binding for global variable ‘value’
summary.subsamples: no visible binding for global variable ‘percent’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [146s/146s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
generateSubsampledMatrix 50.497  0.714  51.255
getSeed                  43.013  0.513  43.528
subsample                42.923  0.564  43.488
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/subSeq.Rcheck/00check.log’
for details.


subSeq.Rcheck/00install.out:

* installing *source* package ‘subSeq’ ...
** 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 (subSeq)

subSeq.Rcheck/subSeq-Ex.timings:

nameusersystemelapsed
combineSubsamples1.1960.0441.241
generateSubsampledMatrix50.497 0.71451.255
getSeed43.013 0.51343.528
plot.subsamples0.0000.0000.001
plot.summary.subsamples0.0010.0000.002
ss2.2270.0402.267
subsample42.923 0.56443.488
summary.subsamples1.9610.0422.001