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BioC 2.14: CHECK report for ggbio on moscato2

This page was generated on 2014-10-08 08:54:20 -0700 (Wed, 08 Oct 2014).

Package 347/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.12.10
Tengfei Yin
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ggbio
Last Changed Rev: 93626 / Revision: 95116
Last Changed Date: 2014-08-26 15:16:30 -0700 (Tue, 26 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: ggbio
Version: 1.12.10
Command: rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.12.10.tar.gz >ggbio-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.12.10.tar.gz
StartedAt: 2014-10-08 01:36:34 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:55:07 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 1112.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ggbio.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.12.10.tar.gz >ggbio-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.12.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/ggbio.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.12.10'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'ggbio' can be installed ... WARNING
Found the following significant warnings:
  Warning: 'eval' is deprecated.
See 'E:/biocbld/bbs-2.14-bioc/meat/ggbio.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'ggplot2:::add_ggplot' 'ggplot2:::cunion' 'ggplot2:::rescale01'
  'ggplot2:::set_last_plot' 'ggplot2:::zeroGrob'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
.combineNames: no visible binding for global variable
  '.layout_circle.geoms'
.combineNames: no visible binding for global variable
  '.layout_circle.stats'
Ideogram: no visible binding for global variable 'ideoCyto'
ScalePlot: no visible binding for global variable 'y'
ScalePlot2: no visible binding for global variable 'breaks'
ScalePlot2: no visible binding for global variable 'yend'
ScalePlot2: no visible binding for global variable 'y.text'
align.plots: no visible binding for global variable 'lgrobs'
alignPlots: no visible binding for global variable 'lgrobs'
bioplot: no visible global function definition for 'autofacets'
bioplot: no visible global function definition for 'normArg_geom'
bioplot: no visible global function definition for 'normArg_mapping'
bioplot: no visible global function definition for 'normArg_facets'
bioplot: no visible global function definition for 'QueryLayer'
getNR: no visible global function definition for 'se'
getNR: no visible global function definition for 'indexProbesProcessed'
getNR: no visible global function definition for 'coefs'
ggsave : default_name: no visible global function definition for
  'digest.ggplot'
plotInter: no visible binding for global variable 'fe'
plotInter: no visible binding for global variable 'value'
plotInter2: no visible binding for global variable 'fe'
plotInter2: no visible binding for global variable 'value'
plotKaryogram: no visible binding for global variable 'cytobands'
plotStackedOverview: no visible binding for global variable 'cytobands'
scale_x_sequnit: no visible binding for global variable '.x'
height,GGbio: no visible binding for global variable 'mt'
height,Tracked: no visible binding for global variable 'mt'
height,gg: no visible binding for global variable 'mt'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '+' and siglist 'Bioplot,ANY'
  generic 'names' and siglist 'Geom'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [367s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
autoplot-method         90.67   0.29   91.47
layout_karyogram-method 38.67   0.01   38.87
tracks                  34.67   0.04   34.72
geom_alignment-method   32.56   0.49   33.04
plotRangesLinkedToData  23.30   0.38   23.68
geom_arrow-method       16.20   0.00   16.19
stat_aggregate-method   14.96   0.00   14.96
ggplot-method           11.55   0.05   11.60
stat_reduce-method      10.21   0.15   10.36
layout_circle-method    10.26   0.02   10.28
plotGrandLinear          8.04   0.06    8.10
stat_bin-method          7.45   0.00    8.03
geom_chevron-method      6.52   0.02    6.53
** running examples for arch 'x64' ... [391s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
autoplot-method         102.55   0.42  102.99
tracks                   38.39   0.05   38.59
layout_karyogram-method  36.30   0.02   36.32
geom_alignment-method    35.57   0.50   36.07
plotRangesLinkedToData   22.57   0.43   22.99
geom_arrow-method        18.05   0.02   18.07
stat_aggregate-method    15.66   0.02   15.69
ggplot-method            12.04   0.00   12.26
layout_circle-method     11.14   0.00   11.14
stat_reduce-method        8.59   0.08    8.67
plotGrandLinear           8.40   0.01    8.41
geom_chevron-method       7.24   0.01    7.25
stat_bin-method           6.76   0.00    6.75
geom_rect-method          5.39   0.00    5.40
scale_fill_giemsa         5.30   0.01    5.32
geom_arrowrect-method     5.27   0.01    5.29
geom_segment-method       5.11   0.00    5.15
* checking for unstated dependencies in tests ... WARNING
'library' or 'require' call not declared from: 'testthat'
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [12s]
 [12s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [13s]
 [14s] 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

WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/ggbio.Rcheck/00check.log'
for details.

ggbio.Rcheck/00install.out:


install for i386

* installing *source* package 'ggbio' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'rescale' in package 'ggbio'
Creating a new generic function for 'xlim' in package 'ggbio'
Creating a generic function for 'print' from package 'base' in package 'ggbio'
Warning: 'eval' is deprecated.
Use 'plotIdeogram' instead.
See help("Deprecated")
Creating a generic function for 'summary' from package 'base' in package 'ggbio'
in method for 'geom_alignment' with signature '"OrganismDb"': no definition for class "OrganismDb"
Creating a new generic function for 'geom_rect' in package 'ggbio'
Creating a new generic function for 'geom_segment' in package 'ggbio'
Creating a new generic function for 'geom_bar' in package 'ggbio'
Creating a new generic function for 'stat_identity' in package 'ggbio'
Creating a new generic function for 'stat_bin' in package 'ggbio'
in method for 'autoplot' with signature '"OrganismDb"': no definition for class "OrganismDb"
Creating a generic function for 'aggregate' from package 'stats' in package 'ggbio'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ggbio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggbio' as ggbio_1.12.10.zip
* DONE (ggbio)

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

nameusersystemelapsed
arrangeGrobByParsingLegend3.730.044.28
autoplot-method90.67 0.2991.47
geom_alignment-method32.56 0.4933.04
geom_arch-method1.920.001.92
geom_arrow-method16.20 0.0016.19
geom_arrowrect-method4.820.004.82
geom_bar-method1.660.011.67
geom_chevron-method6.520.026.53
geom_rect-method4.740.014.76
geom_segment-method4.230.034.26
ggbio-class000
ggplot-method11.55 0.0511.60
layout_circle-method10.26 0.0210.28
layout_karyogram-method38.67 0.0138.87
plotFragLength000
plotGrandLinear8.040.068.10
plotRangesLinkedToData23.30 0.3823.68
plotSingleChrom000
plotSpliceSum000
plotStackedOverview000
rescale-method0.140.000.14
scale_fill_fold_change0.580.010.60
scale_fill_giemsa4.760.054.80
scale_x_sequnit0.360.020.37
stat_aggregate-method14.96 0.0014.96
stat_bin-method7.450.008.03
stat_coverage-method3.730.003.73
stat_gene-method000
stat_identity-method3.900.033.96
stat_reduce-method10.21 0.1510.36
stat_slice-method4.880.004.89
stat_stepping-method3.450.003.44
stat_table-method2.240.032.28
theme2.440.002.43
tracks34.67 0.0434.72

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

nameusersystemelapsed
arrangeGrobByParsingLegend4.370.004.37
autoplot-method102.55 0.42102.99
geom_alignment-method35.57 0.5036.07
geom_arch-method2.10.02.1
geom_arrow-method18.05 0.0218.07
geom_arrowrect-method5.270.015.29
geom_bar-method1.550.021.56
geom_chevron-method7.240.017.25
geom_rect-method5.390.005.40
geom_segment-method5.110.005.15
ggbio-class0.010.000.01
ggplot-method12.04 0.0012.26
layout_circle-method11.14 0.0011.14
layout_karyogram-method36.30 0.0236.32
plotFragLength000
plotGrandLinear8.400.018.41
plotRangesLinkedToData22.57 0.4322.99
plotSingleChrom000
plotSpliceSum000
plotStackedOverview000
rescale-method0.150.000.15
scale_fill_fold_change0.660.000.66
scale_fill_giemsa5.300.015.32
scale_x_sequnit0.440.000.44
stat_aggregate-method15.66 0.0215.69
stat_bin-method6.760.006.75
stat_coverage-method3.540.013.56
stat_gene-method000
stat_identity-method3.680.003.73
stat_reduce-method8.590.088.67
stat_slice-method4.480.004.48
stat_stepping-method4.180.034.21
stat_table-method2.550.002.55
theme2.90.02.9
tracks38.39 0.0538.59