BioC 3.3: CHECK report for cobindR on windows2.bioconductor.org

Package: cobindR

Version: 1.9.0

Command: rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.9.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out && c:\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_1.9.0.tar.gz

StartedAt: 2015-10-27 01:32:33 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:39:46 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 433.2 seconds

RetCode: 0

Status:  OK

CheckDir: cobindR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.9.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out  && c:\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_1.9.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/cobindR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.9.0'
* 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
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'
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.positions,cobindr: no visible binding for global variable 'n.cpu'
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.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'
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'
write.bindingsites.table,cobindr: no visible global function definition
  for 'mcols'
Undefined global functions or variables:
  GADEM GRanges MotifDb error gpar grid.draw grid.newpage grid.text
  grid_legend makePWM mclapply mcols n.cpu nMotifs plot_gene_map
  popViewport pushViewport pwm seqLogo sequence_names sfCpus sfInit
  sfLapply sfStop venn.diagram viewport
* 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' ... [105s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
rtfbs            14.20   0.68   15.09
testCpG          14.53   0.01   14.54
search.pwm       13.84   0.00   13.84
write.sequences   9.51   0.06    9.58
search.gadem      9.50   0.05    9.55
bg_binding_sites  3.73   0.30    5.24
** running examples for arch 'x64' ... [125s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
testCpG          18.89   0.02   18.90
rtfbs            18.00   0.02   18.03
search.pwm       16.79   0.00   16.78
search.gadem     11.29   0.01   11.31
write.sequences  10.96   0.01   10.97
bg_binding_sites  5.14   0.28    5.43
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [6s]
 [6s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [7s]
 [7s] 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
  'c:/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_1.9.0.zip
* DONE (cobindR)

name	user	system	elapsed
SeqObj-class	0	0	0
bg_binding_sites	3.73	0.30	5.24
bg_pairs	3.19	0.00	3.18
bg_sequence_origin	0	0	0
bg_sequence_source	0	0	0
bg_sequence_type	0	0	0
bg_sequences	3.03	0.02	3.05
binding_sites	3.78	0.01	3.79
cobindRConfiguration	0	0	0
cobindr-class	0	0	0
comment	0.05	0.02	0.06
configuration-class	0	0	0
configuration	3.31	0.00	3.31
downstream	0	0	0
experiment_description	3.16	0.00	3.16
fdrThreshold	0.01	0.00	0.01
get.bindingsite.ranges	0	0	0
id	0	0	0
location	0.06	0.01	0.08
mart	0	0	0
max_distance	0.02	0.00	0.02
name	0.08	0.00	0.07
pValue	0	0	0
pairs	0	0	0
pairs_of_interest	3.47	0.00	3.47
path	0	0	0
pfm	2.93	0.02	2.96
pfm_path	0	0	0
plot.gc	4.72	0.05	4.77
pseudocount	0	0	0
rtfbs	14.20	0.68	15.09
search.gadem	9.50	0.05	9.55
search.pwm	13.84	0.00	13.84
seqObj	0.08	0.00	0.08
sequence	0.08	0.00	0.08
sequence_origin	0.02	0.00	0.01
sequence_source	0	0	0
sequence_type	0	0	0
sequences	3.59	0.02	3.61
species	0	0	0
testCpG	14.53	0.01	14.54
threshold	0	0	0
uid	0.06	0.02	0.08
upstream	0.02	0.00	0.02
write.sequences	9.51	0.06	9.58

name	user	system	elapsed
SeqObj-class	0	0	0
bg_binding_sites	5.14	0.28	5.43
bg_pairs	3.82	0.00	3.83
bg_sequence_origin	0	0	0
bg_sequence_source	0	0	0
bg_sequence_type	0	0	0
bg_sequences	4.93	0.00	4.92
binding_sites	3.92	0.00	3.93
cobindRConfiguration	0	0	0
cobindr-class	0	0	0
comment	0.08	0.02	0.09
configuration-class	0	0	0
configuration	3.78	0.00	3.80
downstream	0	0	0
experiment_description	3.54	0.00	3.54
fdrThreshold	0	0	0
get.bindingsite.ranges	0	0	0
id	0	0	0
location	0.08	0.00	0.08
mart	0	0	0
max_distance	0.01	0.00	0.01
name	0.1	0.0	0.1
pValue	0	0	0
pairs	0	0	0
pairs_of_interest	4.25	0.01	4.26
path	0.01	0.00	0.02
pfm	3.55	0.00	3.54
pfm_path	0	0	0
plot.gc	4.92	0.02	4.94
pseudocount	0	0	0
rtfbs	18.00	0.02	18.03
search.gadem	11.29	0.01	11.31
search.pwm	16.79	0.00	16.78
seqObj	0.08	0.00	0.08
sequence	0.08	0.00	0.07
sequence_origin	0.01	0.00	0.02
sequence_source	0	0	0
sequence_type	0	0	0
sequences	3.89	0.00	3.89
species	0	0	0
testCpG	18.89	0.02	18.90
threshold	0.02	0.00	0.02
uid	0.09	0.00	0.09
upstream	0.01	0.00	0.02
write.sequences	10.96	0.01	10.97