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BioC 3.2: CHECK report for cobindR on zin1

This page was generated on 2016-04-23 10:13:12 -0700 (Sat, 23 Apr 2016).

Package 204/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cobindR 1.8.0
Manuela Benary
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/cobindR
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cobindR
Version: 1.8.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.8.0.tar.gz
StartedAt: 2016-04-22 23:24:14 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:28:21 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 246.9 seconds
RetCode: 0
Status:  OK 
CheckDir: cobindR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/cobindR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.8.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cobindR’ can be installed ... [15s/15s] 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 ... [145s/97s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
testCpG          18.074  1.560  13.894
rtfbs            15.698  1.437   8.964
plot.gc           8.071  8.183   7.583
search.pwm       14.124  1.446   9.935
search.gadem     12.582  0.878   9.291
write.sequences  10.649  0.605   8.893
sequences         6.495  0.594   3.316
bg_binding_sites  4.785  0.500   4.180
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [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-3.2-bioc/meat/cobindR.Rcheck/00check.log’
for details.


cobindR.Rcheck/00install.out:

* 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)

cobindR.Rcheck/cobindR-Ex.timings:

nameusersystemelapsed
SeqObj-class0.0010.0000.001
bg_binding_sites4.7850.5004.180
bg_pairs4.1110.5423.309
bg_sequence_origin0.0040.0000.003
bg_sequence_source0.0030.0000.003
bg_sequence_type0.0030.0000.003
bg_sequences4.0090.5073.285
binding_sites4.1950.4853.482
cobindRConfiguration0.0000.0040.004
cobindr-class0.0010.0000.001
comment0.1060.0040.110
configuration-class0.0010.0000.001
configuration3.9610.5363.396
downstream0.0040.0000.004
experiment_description3.7890.4293.240
fdrThreshold0.0030.0000.004
get.bindingsite.ranges0.0010.0000.000
id0.0040.0000.003
location0.1060.0000.107
mart0.0040.0000.003
max_distance0.0030.0000.003
name0.1080.0080.116
pValue0.0030.0000.004
pairs0.0040.0000.003
pairs_of_interest3.8210.4133.213
path0.0030.0000.003
pfm4.3270.6403.157
pfm_path0.0010.0000.003
plot.gc8.0718.1837.583
pseudocount0.0050.0030.004
rtfbs15.698 1.437 8.964
search.gadem12.582 0.878 9.291
search.pwm14.124 1.446 9.935
seqObj0.1290.0000.129
sequence0.1210.0130.133
sequence_origin0.0050.0000.005
sequence_source0.0050.0000.004
sequence_type0.0040.0000.005
sequences6.4950.5943.316
species0.0030.0000.004
testCpG18.074 1.56013.894
threshold0.0030.0000.003
uid0.1050.0000.105
upstream0.0030.0000.003
write.sequences10.649 0.605 8.893