cobindR 1.9.0
Manuela Benary
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cobindR | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/cobindR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cobindR’ can be installed ... [17s/17s] 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: 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 ... [164s/100s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
testCpG 19.359 1.867 13.177
rtfbs 17.716 1.728 9.569
plot.gc 7.888 10.380 8.109
search.gadem 15.909 1.048 10.465
search.pwm 14.996 1.604 9.553
write.sequences 12.899 0.835 9.686
sequences 7.957 0.742 4.067
configuration 5.272 0.873 3.837
bg_sequences 5.041 0.717 4.109
bg_binding_sites 4.882 0.725 3.994
bg_pairs 4.470 0.653 3.421
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [6s/6s]
[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
‘/home/biocbuild/bbs-3.3-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)