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BioC 3.5: CHECK report for heatmaps on malbec2

This page was generated on 2017-08-16 13:18:25 -0400 (Wed, 16 Aug 2017).

Package 619/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
heatmaps 1.0.0
Malcolm Perry
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/heatmaps
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: heatmaps
Version: 1.0.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings heatmaps_1.0.0.tar.gz
StartedAt: 2017-08-15 23:47:45 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:49:54 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 129.0 seconds
RetCode: 0
Status:  OK 
CheckDir: heatmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings heatmaps_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/heatmaps.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘heatmaps/DESCRIPTION’ ... OK
* this is package ‘heatmaps’ version ‘1.0.0’
* 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 ‘heatmaps’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   6.9Mb
* 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
makeGaussian2D: no visible binding for global variable ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘rtracklayer’
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/heatmaps.Rcheck/00check.log’
for details.


heatmaps.Rcheck/00install.out:

* installing *source* package ‘heatmaps’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘scale’ in package ‘heatmaps’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (heatmaps)

heatmaps.Rcheck/heatmaps-Ex.timings:

nameusersystemelapsed
CoverageHeatmap0.2960.0080.301
Heatmap-class0.0080.0000.010
Heatmap0.0120.0000.009
PWMScanHeatmap0.2800.0000.281
PatternHeatmap0.0880.0000.085
coords0.0080.0000.009
default_color0.0040.0000.002
getScale0.0000.0000.001
heatmapOptions0.4560.0240.479
image0.0120.0000.011
label0.0080.0000.008
metadata0.0120.0000.009
nseq0.0080.0000.008
plotHeatmap0.0320.0040.037
plotHeatmapList0.1280.0040.133
plotHeatmapMeta0.0280.0000.029
plotPatternDensityMap0.5240.0000.525
plot_clusters0.0560.0000.059
plot_legend0.2680.0000.271
scale0.0040.0040.008
smoothHeatmap0.0280.0040.045
xm0.0120.0000.012
ym0.0080.0040.010