BioC 3.2: CHECK report for cobindR on windows1.bioconductor.org

Package: cobindR

Version: 1.8.0

Command: rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.8.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.8.0.tar.gz

StartedAt: 2015-10-27 00:46:30 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 00:54:29 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 478.8 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-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.8.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.8.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/cobindR.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.8.0'
* 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 : .local: no visible global function
  definition for 'GRanges'
get.bindingsite.ranges,cobindr : .local: no visible binding for global
  variable 'sequence_names'
get.bindingsite.ranges,cobindr : .local: no visible binding for global
  variable 'pwm'
plot.positions,cobindr : .local: no visible binding for global variable
  'n.cpu'
plot.positions,cobindr : .local: no visible global function definition
  for 'grid.newpage'
plot.positions,cobindr : .local: no visible global function definition
  for 'pushViewport'
plot.positions,cobindr : .local: no visible global function definition
  for 'viewport'
plot.positions,cobindr : .local: no visible global function definition
  for 'plot_gene_map'
plot.positions,cobindr : .local: no visible global function definition
  for 'popViewport'
plot.positions,cobindr : .local: no visible global function definition
  for 'gpar'
plot.positions,cobindr : .local: no visible global function definition
  for 'grid_legend'
plot.tfbs.venndiagram,cobindr : .local: no visible global function
  definition for 'venn.diagram'
plot.tfbs.venndiagram,cobindr : .local: no visible global function
  definition for 'grid.draw'
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
  function definition for 'makePWM'
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
  function definition for 'seqLogo'
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
  function definition for 'grid.text'
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
  function definition for 'gpar'
search.gadem,cobindr : .local : <anonymous>: no visible global function
  definition for 'GADEM'
search.gadem,cobindr : .local: no visible global function definition
  for 'GADEM'
search.gadem,cobindr : .local: no visible global function definition
  for 'nMotifs'
search.pwm,cobindr : .local: no visible global function definition for
  'error'
write.bindingsites.table,cobindr : .local: no visible global function
  definition for 'mcols'
* 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' ... [110s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
testCpG          15.77   0.02   15.78
search.pwm       15.44   0.00   15.46
rtfbs            13.27   0.01   13.36
search.gadem     10.69   0.00   10.69
write.sequences  10.32   0.01   10.33
bg_binding_sites  4.19   0.19    5.31
** running examples for arch 'x64' ... [137s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
testCpG          21.42   0.03   21.45
search.pwm       19.30   0.02   19.33
rtfbs            16.83   0.03   16.86
search.gadem     13.79   0.00   13.80
write.sequences  13.02   0.00   13.02
bg_binding_sites  4.91   0.23    5.14
plot.gc           5.08   0.04    5.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [7s]
 [7s] 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-3.2-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_1.8.0.zip
* DONE (cobindR)

name	user	system	elapsed
SeqObj-class	0	0	0
bg_binding_sites	4.19	0.19	5.31
bg_pairs	3.16	0.00	3.16
bg_sequence_origin	0	0	0
bg_sequence_source	0.01	0.00	0.02
bg_sequence_type	0	0	0
bg_sequences	3.11	0.01	3.12
binding_sites	3.38	0.00	3.38
cobindRConfiguration	0	0	0
cobindr-class	0	0	0
comment	0.12	0.00	0.12
configuration-class	0	0	0
configuration	3.39	0.06	3.45
downstream	0	0	0
experiment_description	3.63	0.00	3.63
fdrThreshold	0	0	0
get.bindingsite.ranges	0	0	0
id	0.01	0.00	0.01
location	0.08	0.02	0.10
mart	0	0	0
max_distance	0	0	0
name	0.11	0.00	0.11
pValue	0	0	0
pairs	0.01	0.00	0.02
pairs_of_interest	3.10	0.00	3.09
path	0	0	0
pfm	4.13	0.02	4.14
pfm_path	0	0	0
plot.gc	4.34	0.01	4.37
pseudocount	0	0	0
rtfbs	13.27	0.01	13.36
search.gadem	10.69	0.00	10.69
search.pwm	15.44	0.00	15.46
seqObj	0.12	0.00	0.12
sequence	0.11	0.00	0.11
sequence_origin	0	0	0
sequence_source	0	0	0
sequence_type	0	0	0
sequences	4.14	0.00	4.14
species	0.01	0.00	0.01
testCpG	15.77	0.02	15.78
threshold	0	0	0
uid	0.11	0.00	0.11
upstream	0	0	0
write.sequences	10.32	0.01	10.33

name	user	system	elapsed
SeqObj-class	0	0	0
bg_binding_sites	4.91	0.23	5.14
bg_pairs	4.11	0.00	4.11
bg_sequence_origin	0	0	0
bg_sequence_source	0.00	0.02	0.01
bg_sequence_type	0	0	0
bg_sequences	4.80	0.03	4.83
binding_sites	4.39	0.00	4.39
cobindRConfiguration	0	0	0
cobindr-class	0.01	0.00	0.02
comment	0.17	0.00	0.17
configuration-class	0	0	0
configuration	4.34	0.00	4.35
downstream	0	0	0
experiment_description	4.96	0.00	4.95
fdrThreshold	0.01	0.00	0.02
get.bindingsite.ranges	0	0	0
id	0	0	0
location	0.15	0.01	0.17
mart	0.00	0.02	0.02
max_distance	0	0	0
name	0.19	0.00	0.19
pValue	0	0	0
pairs	0.01	0.00	0.02
pairs_of_interest	4.14	0.00	4.14
path	0.02	0.00	0.01
pfm	3.75	0.02	3.77
pfm_path	0	0	0
plot.gc	5.08	0.04	5.14
pseudocount	0	0	0
rtfbs	16.83	0.03	16.86
search.gadem	13.79	0.00	13.80
search.pwm	19.30	0.02	19.33
seqObj	0.11	0.00	0.11
sequence	0.08	0.05	0.12
sequence_origin	0	0	0
sequence_source	0	0	0
sequence_type	0.01	0.00	0.02
sequences	3.99	0.00	3.98
species	0	0	0
testCpG	21.42	0.03	21.45
threshold	0.02	0.00	0.02
uid	0.12	0.00	0.12
upstream	0	0	0
write.sequences	13.02	0.00	13.02