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BioC 3.5: CHECK report for cobindR on malbec2

This page was generated on 2017-08-16 13:15:09 -0400 (Wed, 16 Aug 2017).

Package 255/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cobindR 1.14.0
Manuela Benary
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/cobindR
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: cobindR
Version: 1.14.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.14.0.tar.gz
StartedAt: 2017-08-15 22:05:27 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:10:03 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 276.2 seconds
RetCode: 0
Status:  OK 
CheckDir: cobindR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/cobindR.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 ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘genoPlotR’
* 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 ‘cobindR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘MotifDb’ ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compare.samples: no visible global function definition for
  ‘wilcox.test’
input.pfm.similarity: no visible global function definition for ‘combn’
parallelize: no visible global function definition for
  ‘installed.packages’
parallelize: no visible global function definition for ‘mclapply’
parallelize: no visible global function definition for ‘sfCpus’
parallelize: no visible global function definition for ‘sfInit’
parallelize: no visible global function definition for ‘sfLapply’
parallelize: no visible global function definition for ‘sfStop’
query.motifDb: no visible binding for global variable ‘MotifDb’
find.pairs,cobindr: no visible global function definition for ‘combn’
get.bindingsite.ranges,cobindr: no visible global function definition
  for ‘GRanges’
get.bindingsite.ranges,cobindr: no visible binding for global variable
  ‘sequence_names’
get.bindingsite.ranges,cobindr: no visible binding for global variable
  ‘pwm’
plot.detrending,cobindr: no visible global function definition for
  ‘par’
plot.detrending,cobindr: no visible global function definition for
  ‘plot’
plot.detrending,cobindr: no visible global function definition for
  ‘lines’
plot.detrending,cobindr: no visible global function definition for
  ‘title’
plot.gc,cobindr: no visible global function definition for
  ‘txtProgressBar’
plot.gc,cobindr: no visible global function definition for
  ‘setTxtProgressBar’
plot.gc,cobindr: no visible global function definition for ‘rainbow’
plot.gc,cobindr: no visible global function definition for ‘par’
plot.gc,cobindr: no visible global function definition for ‘matplot’
plot.gc,cobindr: no visible global function definition for ‘points’
plot.gc,cobindr: no visible global function definition for ‘legend’
plot.pairdistance,cobindr: no visible global function definition for
  ‘hist’
plot.pairdistribution,cobindr: no visible global function definition
  for ‘plot’
plot.positionprofile,cobindr: no visible global function definition for
  ‘rainbow’
plot.positionprofile,cobindr: no visible global function definition for
  ‘matplot’
plot.positionprofile,cobindr: no visible global function definition for
  ‘legend’
plot.positions.simple,cobindr: no visible global function definition
  for ‘rainbow’
plot.positions.simple,cobindr: no visible global function definition
  for ‘par’
plot.positions.simple,cobindr: no visible global function definition
  for ‘plot’
plot.positions.simple,cobindr: no visible global function definition
  for ‘points’
plot.positions.simple,cobindr: no visible global function definition
  for ‘legend’
plot.positions,cobindr: no visible global function definition for
  ‘rainbow’
plot.positions,cobindr: no visible binding for global variable ‘n.cpu’
plot.positions,cobindr: no visible global function definition for
  ‘hclust’
plot.positions,cobindr: no visible global function definition for
  ‘dist’
plot.positions,cobindr: no visible global function definition for
  ‘order.dendrogram’
plot.positions,cobindr: no visible global function definition for
  ‘as.dendrogram’
plot.positions,cobindr: no visible global function definition for
  ‘grid.newpage’
plot.positions,cobindr: no visible global function definition for
  ‘pushViewport’
plot.positions,cobindr: no visible global function definition for
  ‘viewport’
plot.positions,cobindr: no visible global function definition for
  ‘plot_gene_map’
plot.positions,cobindr: no visible global function definition for
  ‘popViewport’
plot.positions,cobindr: no visible global function definition for
  ‘gpar’
plot.positions,cobindr: no visible global function definition for
  ‘grid_legend’
plot.tfbs.heatmap,cobindr: no visible global function definition for
  ‘phyper’
plot.tfbs.heatmap,cobindr: no visible global function definition for
  ‘heat.colors’
plot.tfbs.venndiagram,cobindr: no visible global function definition
  for ‘venn.diagram’
plot.tfbs.venndiagram,cobindr: no visible global function definition
  for ‘grid.draw’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
  definition for ‘makePWM’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
  definition for ‘seqLogo’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
  definition for ‘grid.text’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
  definition for ‘gpar’
read.pfm,configuration: no visible global function definition for
  ‘read.table’
read.sequences,configuration: no visible global function definition for
  ‘txtProgressBar’
read.sequences,configuration: no visible global function definition for
  ‘setTxtProgressBar’
read.sequences,configuration: no visible global function definition for
  ‘read.table’
search.gadem,cobindr : <anonymous>: no visible global function
  definition for ‘GADEM’
search.gadem,cobindr: no visible global function definition for ‘GADEM’
search.gadem,cobindr: no visible global function definition for
  ‘nMotifs’
search.pwm,cobindr: no visible global function definition for ‘error’
testCpG,cobindr: no visible global function definition for ‘hist’
testCpG,cobindr: no visible global function definition for ‘layout’
testCpG,cobindr: no visible global function definition for ‘par’
testCpG,cobindr: no visible global function definition for ‘barplot’
write.bindingsites.table,cobindr: no visible global function definition
  for ‘mcols’
write.bindingsites.table,cobindr: no visible global function definition
  for ‘write.table’
write.bindingsites,cobindr: no visible global function definition for
  ‘write.table’
write,cobindr-character: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  GADEM GRanges MotifDb as.dendrogram barplot combn dist error gpar
  grid.draw grid.newpage grid.text grid_legend hclust heat.colors hist
  installed.packages layout legend lines makePWM matplot mclapply mcols
  n.cpu nMotifs order.dendrogram par phyper plot plot_gene_map points
  popViewport pushViewport pwm rainbow read.table seqLogo
  sequence_names setTxtProgressBar sfCpus sfInit sfLapply sfStop title
  txtProgressBar venn.diagram viewport wilcox.test write.table
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "hist", "layout", "legend", "lines",
             "matplot", "par", "plot", "points", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "phyper", "wilcox.test")
  importFrom("utils", "combn", "installed.packages", "read.table",
             "setTxtProgressBar", "txtProgressBar", "write.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plot.gc          10.576 25.292  16.034
rtfbs            17.204  4.408   7.049
testCpG          14.556  3.308   9.882
search.pwm       13.112  3.060   8.765
search.gadem     11.292  2.344   6.782
write.sequences   8.528  2.112   5.308
sequences         6.640  1.344   2.787
bg_binding_sites  4.444  1.112   6.176
configuration     3.556  1.472   2.551
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/cobindR.Rcheck/00check.log’
for details.


cobindR.Rcheck/00install.out:

* installing *source* package ‘cobindR’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘sequence’ in package ‘cobindR’
Creating a generic function for ‘write’ from package ‘base’ in package ‘cobindR’
Creating a generic function for ‘write.fasta’ from package ‘seqinr’ in package ‘cobindR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cobindR)

cobindR.Rcheck/cobindR-Ex.timings:

nameusersystemelapsed
SeqObj-class0.0040.0000.001
bg_binding_sites4.4441.1126.176
bg_pairs3.5441.1002.603
bg_sequence_origin0.0040.0000.003
bg_sequence_source0.0040.0000.002
bg_sequence_type0.0040.0000.002
bg_sequences3.2801.1442.475
binding_sites3.0921.2402.141
cobindRConfiguration0.0040.0000.002
cobindr-class0.0000.0000.001
comment0.0840.0000.084
configuration-class0.0040.0000.001
configuration3.5561.4722.551
downstream0.0040.0000.003
experiment_description3.2321.3482.307
fdrThreshold0.0000.0000.003
get.bindingsite.ranges000
id0.0000.0000.002
location0.0880.0040.094
mart0.0040.0000.003
max_distance0.0040.0000.004
name0.0840.0000.086
pValue0.0000.0000.003
pairs0.0040.0000.003
pairs_of_interest3.2881.1562.475
path0.0000.0040.003
pfm3.6001.1122.889
pfm_path0.0040.0000.004
plot.gc10.57625.29216.034
pseudocount0.0040.0000.004
rtfbs17.204 4.408 7.049
search.gadem11.292 2.344 6.782
search.pwm13.112 3.060 8.765
seqObj0.1040.0120.118
sequence0.0720.0080.083
sequence_origin0.0040.0000.003
sequence_source0.0000.0000.002
sequence_type0.0000.0000.002
sequences6.6401.3442.787
species0.0040.0000.002
testCpG14.556 3.308 9.882
threshold0.0040.0000.003
uid0.0840.0040.088
upstream0.0000.0040.002
write.sequences8.5282.1125.308