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BioC 3.2: CHECK report for cobindR on moscato1

This page was generated on 2016-04-23 10:19:30 -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: rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.8.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.8.0.tar.gz
StartedAt: 2016-04-23 00:56:37 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:09:00 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 742.6 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.8.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/cobindR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.8.0'
* 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 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [163s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
testCpG          21.80   0.02   21.80
search.pwm       19.81   0.00   21.25
rtfbs            19.36   0.05   24.26
search.gadem     14.90   0.02   14.91
write.sequences  12.45   0.01   12.46
plot.gc           7.08   0.06    7.60
bg_binding_sites  6.08   0.29    6.74
bg_sequences      5.74   0.02    5.76
bg_pairs          5.38   0.00    5.39
** running examples for arch 'x64' ... [210s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
testCpG                31.75   0.04   31.77
rtfbs                  30.92   0.03   32.13
search.pwm             27.99   0.00   28.09
search.gadem           22.44   0.00   22.43
write.sequences        17.96   0.00   17.95
plot.gc                 8.58   0.06    8.75
pairs_of_interest       6.99   0.02    7.01
bg_binding_sites        6.59   0.31    6.97
pfm                     6.80   0.00    6.80
configuration           6.71   0.00    6.71
binding_sites           6.53   0.00    6.53
sequences               6.05   0.00    6.13
bg_sequences            5.59   0.05    5.89
bg_pairs                5.32   0.00    5.32
experiment_description  5.18   0.01    5.20
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [11s]
 [11s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [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
  'D:/biocbld/bbs-3.2-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_1.8.0.zip
* DONE (cobindR)

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

nameusersystemelapsed
SeqObj-class000
bg_binding_sites6.080.296.74
bg_pairs5.380.005.39
bg_sequence_origin000
bg_sequence_source000
bg_sequence_type0.020.000.01
bg_sequences5.740.025.76
binding_sites4.580.004.58
cobindRConfiguration000
cobindr-class000
comment0.160.000.16
configuration-class000
configuration4.510.004.51
downstream000
experiment_description4.330.024.34
fdrThreshold000
get.bindingsite.ranges000
id0.010.000.02
location0.140.000.14
mart0.020.000.01
max_distance000
name0.180.010.21
pValue0.020.000.01
pairs000
pairs_of_interest4.850.004.85
path000
pfm4.530.004.59
pfm_path000
plot.gc7.080.067.60
pseudocount0.010.000.01
rtfbs19.36 0.0524.26
search.gadem14.90 0.0214.91
search.pwm19.81 0.0021.25
seqObj0.150.000.14
sequence0.120.030.16
sequence_origin000
sequence_source000
sequence_type000
sequences4.450.004.45
species0.010.000.02
testCpG21.80 0.0221.80
threshold000
uid0.220.000.22
upstream000
write.sequences12.45 0.0112.46

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

nameusersystemelapsed
SeqObj-class000
bg_binding_sites6.590.316.97
bg_pairs5.320.005.32
bg_sequence_origin0.020.000.02
bg_sequence_source000
bg_sequence_type0.010.000.02
bg_sequences5.590.055.89
binding_sites6.530.006.53
cobindRConfiguration0.010.000.02
cobindr-class000
comment0.190.030.22
configuration-class000
configuration6.710.006.71
downstream000
experiment_description5.180.015.20
fdrThreshold0.020.000.01
get.bindingsite.ranges000
id000
location0.140.020.16
mart000
max_distance0.020.000.02
name0.220.000.22
pValue0.010.000.01
pairs000
pairs_of_interest6.990.027.01
path000
pfm6.80.06.8
pfm_path000
plot.gc8.580.068.75
pseudocount0.020.000.02
rtfbs30.92 0.0332.13
search.gadem22.44 0.0022.43
search.pwm27.99 0.0028.09
seqObj0.160.000.15
sequence0.140.000.15
sequence_origin000
sequence_source000
sequence_type000
sequences6.050.006.13
species000
testCpG31.75 0.0431.77
threshold0.010.000.02
uid0.110.030.14
upstream000
write.sequences17.96 0.0017.95