cobindR 1.7.1
Manuela Benary
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cobindR | | Last Changed Rev: 104973 / Revision: 107696 | | Last Changed Date: 2015-06-15 08:47:13 -0700 (Mon, 15 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cobindR_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/cobindR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.7.1’
* 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 ... [22s/22s] 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
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [229s/158s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
testCpG 27.181 4.301 21.397
rtfbs 22.354 3.453 13.650
plot.gc 13.694 11.071 7.783
search.pwm 18.492 3.141 16.398
search.gadem 16.713 1.423 14.098
sequences 13.756 1.452 4.969
write.sequences 12.563 0.667 13.765
experiment_description 7.311 2.024 5.298
bg_sequences 7.346 1.881 5.306
binding_sites 6.577 1.530 5.281
bg_pairs 6.193 1.388 5.255
pairs_of_interest 5.989 1.187 5.864
bg_binding_sites 5.913 0.806 15.520
pfm 5.008 0.776 5.090
configuration 5.044 0.731 4.922
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [10s/11s]
[10s/11s] 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/cobindR.Rcheck/00check.log’
for details.
* 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)