BioC 3.3: CHECK report for cobindR on moscato2

Package: cobindR

Version: 1.10.0

Command: rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.10.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.10.0.tar.gz

StartedAt: 2016-10-13 02:22:11 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:33:45 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 694.5 seconds

RetCode: 0

Status:  OK

CheckDir: cobindR.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.10.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.10.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/cobindR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cobindR/DESCRIPTION' ... OK
* this is package 'cobindR' version '1.10.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
testCpG           24.41   0.00   24.41
search.pwm        20.56   0.02   21.77
rtfbs             18.22   0.00   21.91
search.gadem      15.77   0.04   15.85
write.sequences   15.15   0.05   15.54
sequences          6.01   0.00    6.01
bg_binding_sites   5.46   0.20    7.04
plot.gc            5.60   0.02    7.32
pairs_of_interest  5.16   0.00    5.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
testCpG                28.62   0.03   28.66
rtfbs                  28.43   0.05   28.55
search.pwm             25.16   0.04   25.75
write.sequences        18.58   0.01   18.59
search.gadem           16.01   0.03   16.09
plot.gc                 9.64   0.09    9.73
bg_binding_sites        7.34   0.26    8.34
experiment_description  7.18   0.02    7.19
configuration           6.99   0.00    6.99
pairs_of_interest       6.94   0.05    6.99
bg_pairs                6.94   0.00    6.94
pfm                     6.52   0.00    6.52
bg_sequences            6.39   0.00    6.40
binding_sites           6.32   0.00    6.32
sequences               6.18   0.00    6.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/cobindR.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'cobindR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cobindR' as cobindR_1.10.0.zip
* DONE (cobindR)

name	user	system	elapsed
SeqObj-class	0	0	0
bg_binding_sites	5.46	0.20	7.04
bg_pairs	4.47	0.00	4.47
bg_sequence_origin	0	0	0
bg_sequence_source	0.02	0.00	0.02
bg_sequence_type	0	0	0
bg_sequences	4.52	0.00	4.52
binding_sites	3.96	0.00	3.97
cobindRConfiguration	0	0	0
cobindr-class	0	0	0
comment	0.10	0.00	0.09
configuration-class	0	0	0
configuration	4.29	0.00	4.29
downstream	0.02	0.00	0.01
experiment_description	4.01	0.00	4.01
fdrThreshold	0	0	0
get.bindingsite.ranges	0	0	0
id	0	0	0
location	0.12	0.01	0.14
mart	0	0	0
max_distance	0	0	0
name	0.17	0.00	0.17
pValue	0.02	0.00	0.02
pairs	0	0	0
pairs_of_interest	5.16	0.00	5.16
path	0.02	0.00	0.02
pfm	4.77	0.00	4.77
pfm_path	0	0	0
plot.gc	5.60	0.02	7.32
pseudocount	0.02	0.00	0.01
rtfbs	18.22	0.00	21.91
search.gadem	15.77	0.04	15.85
search.pwm	20.56	0.02	21.77
seqObj	0.11	0.01	0.12
sequence	0.14	0.00	0.14
sequence_origin	0.02	0.00	0.02
sequence_source	0	0	0
sequence_type	0.01	0.00	0.01
sequences	6.01	0.00	6.01
species	0	0	0
testCpG	24.41	0.00	24.41
threshold	0	0	0
uid	0.08	0.02	0.10
upstream	0	0	0
write.sequences	15.15	0.05	15.54

name	user	system	elapsed
SeqObj-class	0	0	0
bg_binding_sites	7.34	0.26	8.34
bg_pairs	6.94	0.00	6.94
bg_sequence_origin	0.02	0.00	0.02
bg_sequence_source	0.02	0.00	0.01
bg_sequence_type	0	0	0
bg_sequences	6.39	0.00	6.40
binding_sites	6.32	0.00	6.32
cobindRConfiguration	0	0	0
cobindr-class	0	0	0
comment	0.09	0.03	0.13
configuration-class	0	0	0
configuration	6.99	0.00	6.99
downstream	0.02	0.00	0.02
experiment_description	7.18	0.02	7.19
fdrThreshold	0	0	0
get.bindingsite.ranges	0	0	0
id	0.02	0.00	0.01
location	0.15	0.00	0.16
mart	0	0	0
max_distance	0.02	0.00	0.01
name	0.15	0.00	0.16
pValue	0	0	0
pairs	0.02	0.00	0.02
pairs_of_interest	6.94	0.05	6.99
path	0	0	0
pfm	6.52	0.00	6.52
pfm_path	0	0	0
plot.gc	9.64	0.09	9.73
pseudocount	0.01	0.00	0.02
rtfbs	28.43	0.05	28.55
search.gadem	16.01	0.03	16.09
search.pwm	25.16	0.04	25.75
seqObj	0.12	0.02	0.14
sequence	0.14	0.00	0.14
sequence_origin	0.02	0.00	0.02
sequence_source	0	0	0
sequence_type	0.01	0.00	0.01
sequences	6.18	0.00	6.18
species	0.02	0.00	0.01
testCpG	28.62	0.03	28.66
threshold	0.02	0.00	0.02
uid	0.08	0.02	0.09
upstream	0.01	0.00	0.02
write.sequences	18.58	0.01	18.59