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BioC 3.6: CHECK report for cobindR on tokay1

This page was generated on 2017-08-16 13:31:42 -0400 (Wed, 16 Aug 2017).

Package 258/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cobindR 1.15.0
Manuela Benary
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cobindR
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cobindR
Version: 1.15.0
Command: rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.15.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.15.0.tar.gz
StartedAt: 2017-08-15 22:33:02 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:41:40 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 517.7 seconds
RetCode: 0
Status:  OK  
CheckDir: cobindR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.15.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cobindR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.15.0'
* 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
compare.samples: no visible global function definition for
  'wilcox.test'
input.pfm.similarity: no visible global function definition for 'combn'
parallelize: no visible global function definition for
  'installed.packages'
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'
find.pairs,cobindr: no visible global function definition for 'combn'
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.detrending,cobindr: no visible global function definition for
  'par'
plot.detrending,cobindr: no visible global function definition for
  'plot'
plot.detrending,cobindr: no visible global function definition for
  'lines'
plot.detrending,cobindr: no visible global function definition for
  'title'
plot.gc,cobindr: no visible global function definition for
  'txtProgressBar'
plot.gc,cobindr: no visible global function definition for
  'setTxtProgressBar'
plot.gc,cobindr: no visible global function definition for 'rainbow'
plot.gc,cobindr: no visible global function definition for 'par'
plot.gc,cobindr: no visible global function definition for 'matplot'
plot.gc,cobindr: no visible global function definition for 'points'
plot.gc,cobindr: no visible global function definition for 'legend'
plot.pairdistance,cobindr: no visible global function definition for
  'hist'
plot.pairdistribution,cobindr: no visible global function definition
  for 'plot'
plot.positionprofile,cobindr: no visible global function definition for
  'rainbow'
plot.positionprofile,cobindr: no visible global function definition for
  'matplot'
plot.positionprofile,cobindr: no visible global function definition for
  'legend'
plot.positions.simple,cobindr: no visible global function definition
  for 'rainbow'
plot.positions.simple,cobindr: no visible global function definition
  for 'par'
plot.positions.simple,cobindr: no visible global function definition
  for 'plot'
plot.positions.simple,cobindr: no visible global function definition
  for 'points'
plot.positions.simple,cobindr: no visible global function definition
  for 'legend'
plot.positions,cobindr: no visible global function definition for
  'rainbow'
plot.positions,cobindr: no visible binding for global variable 'n.cpu'
plot.positions,cobindr: no visible global function definition for
  'hclust'
plot.positions,cobindr: no visible global function definition for
  'dist'
plot.positions,cobindr: no visible global function definition for
  'order.dendrogram'
plot.positions,cobindr: no visible global function definition for
  'as.dendrogram'
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.heatmap,cobindr: no visible global function definition for
  'phyper'
plot.tfbs.heatmap,cobindr: no visible global function definition for
  'heat.colors'
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'
read.pfm,configuration: no visible global function definition for
  'read.table'
read.sequences,configuration: no visible global function definition for
  'txtProgressBar'
read.sequences,configuration: no visible global function definition for
  'setTxtProgressBar'
read.sequences,configuration: no visible global function definition for
  'read.table'
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'
testCpG,cobindr: no visible global function definition for 'hist'
testCpG,cobindr: no visible global function definition for 'layout'
testCpG,cobindr: no visible global function definition for 'par'
testCpG,cobindr: no visible global function definition for 'barplot'
write.bindingsites.table,cobindr: no visible global function definition
  for 'mcols'
write.bindingsites.table,cobindr: no visible global function definition
  for 'write.table'
write.bindingsites,cobindr: no visible global function definition for
  'write.table'
write,cobindr-character: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  GADEM GRanges MotifDb as.dendrogram barplot combn dist error gpar
  grid.draw grid.newpage grid.text grid_legend hclust heat.colors hist
  installed.packages layout legend lines makePWM matplot mclapply mcols
  n.cpu nMotifs order.dendrogram par phyper plot plot_gene_map points
  popViewport pushViewport pwm rainbow read.table seqLogo
  sequence_names setTxtProgressBar sfCpus sfInit sfLapply sfStop title
  txtProgressBar venn.diagram viewport wilcox.test write.table
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "hist", "layout", "legend", "lines",
             "matplot", "par", "plot", "points", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "phyper", "wilcox.test")
  importFrom("utils", "combn", "installed.packages", "read.table",
             "setTxtProgressBar", "txtProgressBar", "write.table")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
testCpG         13.34   0.02   13.35
search.pwm      12.46   0.04   12.50
rtfbs            9.86   0.03   10.40
search.gadem     7.02   0.10    7.10
write.sequences  7.05   0.06    7.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
testCpG         20.45   0.00   20.45
rtfbs           16.00   0.02   16.12
search.pwm      15.28   0.01   15.43
write.sequences 10.77   0.03   10.80
search.gadem    10.14   0.02   10.17
plot.gc          5.00   0.03    5.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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:/Users/biocbuild/bbs-3.6-bioc/meat/cobindR.Rcheck/00check.log'
for details.


cobindR.Rcheck/00install.out:


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_1.15.0.zip
* DONE (cobindR)

cobindR.Rcheck/examples_i386/cobindR-Ex.timings:

nameusersystemelapsed
SeqObj-class000
bg_binding_sites3.050.193.23
bg_pairs2.720.012.73
bg_sequence_origin000
bg_sequence_source000
bg_sequence_type000
bg_sequences2.620.002.62
binding_sites2.720.052.77
cobindRConfiguration000
cobindr-class000
comment0.070.050.12
configuration-class000
configuration2.360.012.38
downstream000
experiment_description2.280.002.28
fdrThreshold000
get.bindingsite.ranges000
id000
location0.080.020.09
mart000
max_distance0.020.000.02
name0.060.010.07
pValue0.000.020.02
pairs000
pairs_of_interest2.250.002.25
path000
pfm2.330.002.33
pfm_path000
plot.gc3.730.033.79
pseudocount000
rtfbs 9.86 0.0310.40
search.gadem7.020.107.10
search.pwm12.46 0.0412.50
seqObj0.080.020.09
sequence0.090.000.10
sequence_origin000
sequence_source000
sequence_type0.010.000.01
sequences2.410.012.43
species000
testCpG13.34 0.0213.35
threshold000
uid0.080.000.08
upstream000
write.sequences7.050.067.11

cobindR.Rcheck/examples_x64/cobindR-Ex.timings:

nameusersystemelapsed
SeqObj-class000
bg_binding_sites4.220.284.52
bg_pairs3.840.023.86
bg_sequence_origin000
bg_sequence_source000
bg_sequence_type000
bg_sequences2.820.012.83
binding_sites3.010.003.01
cobindRConfiguration000
cobindr-class000
comment0.110.000.11
configuration-class000
configuration3.670.003.67
downstream000
experiment_description3.040.003.03
fdrThreshold000
get.bindingsite.ranges000
id000
location0.090.000.10
mart000
max_distance000
name0.10.00.1
pValue0.010.000.01
pairs000
pairs_of_interest2.970.002.97
path000
pfm3.220.003.22
pfm_path000
plot.gc5.000.035.03
pseudocount0.020.000.02
rtfbs16.00 0.0216.12
search.gadem10.14 0.0210.17
search.pwm15.28 0.0115.43
seqObj0.110.000.10
sequence0.110.000.11
sequence_origin000
sequence_source0.010.000.01
sequence_type000
sequences3.990.004.00
species000
testCpG20.45 0.0020.45
threshold000
uid0.110.020.13
upstream000
write.sequences10.77 0.0310.80