BioC 2.14: CHECK report for cobindR on moscato2

Package: cobindR

Version: 1.2.0

Command: rm -rf cobindR.buildbin-libdir && mkdir cobindR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.2.0.tar.gz >cobindR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.2.0.tar.gz

StartedAt: 2014-10-08 00:05:30 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:15:49 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 618.9 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 && mkdir cobindR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.2.0.tar.gz >cobindR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.2.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/cobindR.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cobindR/DESCRIPTION' ... OK
* this is package 'cobindR' version '1.2.0'
* 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 ... 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
* 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 ... OK
* 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 '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'
* 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' ... [176s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
testCpG                26.89   0.00   26.91
search.pwm             25.76   0.00   25.83
rtfbs                  21.81   0.05   21.95
search.gadem           18.57   0.00   18.58
write.sequences        15.35   0.00   15.35
plot.gc                 7.52   0.02    7.57
bg_binding_sites        6.26   0.19    7.19
bg_pairs                5.88   0.01    5.90
binding_sites           5.75   0.00    5.76
configuration           5.64   0.00    5.65
sequences               5.52   0.00    5.52
bg_sequences            5.43   0.02    5.45
pfm                     5.34   0.01    5.35
experiment_description  5.32   0.00    5.43
pairs_of_interest       5.29   0.00    5.29
** running examples for arch 'x64' ... [206s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
testCpG                34.69   0.02   34.72
search.pwm             30.35   0.03   30.48
rtfbs                  25.65   0.00   25.74
search.gadem           20.07   0.00   20.08
write.sequences        18.66   0.02   18.67
plot.gc                 8.83   0.03    8.91
bg_binding_sites        7.16   0.21    7.44
pfm                     6.88   0.00    6.88
bg_pairs                6.63   0.00    6.63
experiment_description  6.52   0.02    6.54
sequences               6.36   0.00    6.36
binding_sites           6.25   0.00    6.25
pairs_of_interest       6.21   0.02    6.22
configuration           6.10   0.00    6.09
bg_sequences            6.07   0.00    6.07
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [7s]
 [8s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [8s]
 [8s] 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-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_1.2.0.zip
* DONE (cobindR)

name	user	system	elapsed
SeqObj-class	0	0	0
bg_binding_sites	6.26	0.19	7.19
bg_pairs	5.88	0.01	5.90
bg_sequence_origin	0	0	0
bg_sequence_source	0.02	0.00	0.01
bg_sequence_type	0	0	0
bg_sequences	5.43	0.02	5.45
binding_sites	5.75	0.00	5.76
cobindRConfiguration	0.02	0.00	0.01
cobindr-class	0	0	0
comment	0.19	0.00	0.19
configuration-class	0	0	0
configuration	5.64	0.00	5.65
downstream	0.02	0.00	0.01
experiment_description	5.32	0.00	5.43
fdrThreshold	0	0	0
get.bindingsite.ranges	0	0	0
id	0.02	0.00	0.01
location	0.12	0.00	0.13
mart	0	0	0
max_distance	0	0	0
name	0.11	0.00	0.13
pValue	0.02	0.00	0.02
pairs	0	0	0
pairs_of_interest	5.29	0.00	5.29
path	0.01	0.00	0.01
pfm	5.34	0.01	5.35
pfm_path	0	0	0
plot.gc	7.52	0.02	7.57
pseudocount	0.01	0.00	0.01
rtfbs	21.81	0.05	21.95
search.gadem	18.57	0.00	18.58
search.pwm	25.76	0.00	25.83
seqObj	0.12	0.01	0.14
sequence	0.17	0.03	0.21
sequence_origin	0	0	0
sequence_source	0	0	0
sequence_type	0.01	0.00	0.01
sequences	5.52	0.00	5.52
species	0.02	0.00	0.02
testCpG	26.89	0.00	26.91
threshold	0.02	0.00	0.02
uid	0.12	0.00	0.12
upstream	0	0	0
write.sequences	15.35	0.00	15.35

name	user	system	elapsed
SeqObj-class	0.02	0.00	0.02
bg_binding_sites	7.16	0.21	7.44
bg_pairs	6.63	0.00	6.63
bg_sequence_origin	0.01	0.00	0.01
bg_sequence_source	0	0	0
bg_sequence_type	0.02	0.00	0.02
bg_sequences	6.07	0.00	6.07
binding_sites	6.25	0.00	6.25
cobindRConfiguration	0.02	0.00	0.02
cobindr-class	0	0	0
comment	0.12	0.02	0.14
configuration-class	0	0	0
configuration	6.10	0.00	6.09
downstream	0	0	0
experiment_description	6.52	0.02	6.54
fdrThreshold	0.02	0.00	0.01
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	0.14	0.02	0.15
pValue	0	0	0
pairs	0	0	0
pairs_of_interest	6.21	0.02	6.22
path	0	0	0
pfm	6.88	0.00	6.88
pfm_path	0	0	0
plot.gc	8.83	0.03	8.91
pseudocount	0.01	0.00	0.02
rtfbs	25.65	0.00	25.74
search.gadem	20.07	0.00	20.08
search.pwm	30.35	0.03	30.48
seqObj	0.13	0.00	0.12
sequence	0.13	0.00	0.12
sequence_origin	0.01	0.00	0.02
sequence_source	0	0	0
sequence_type	0	0	0
sequences	6.36	0.00	6.36
species	0.02	0.00	0.02
testCpG	34.69	0.02	34.72
threshold	0	0	0
uid	0.11	0.01	0.12
upstream	0	0	0
write.sequences	18.66	0.02	18.67