ggbio 1.14.0
Tengfei Yin
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ggbio | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### rm -rf ggbio.buildbin-libdir ggbio.Rcheck && mkdir ggbio.buildbin-libdir ggbio.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.14.0.tar.gz >ggbio.Rcheck\00install.out 2>&1 && cp ggbio.Rcheck\00install.out ggbio-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.14.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ggbio.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.14.0'
* 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 'D:/biocbld/bbs-3.0-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.
* 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'
Ideogram: no visible binding for global variable 'cytobands'
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 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [378s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 87.97 0.56 90.15
tracks 45.99 0.03 46.05
layout_karyogram-method 38.67 0.00 39.82
geom_alignment-method 25.92 0.45 26.38
geom_arrow-method 19.45 0.08 20.89
plotRangesLinkedToData 16.70 0.19 16.88
stat_aggregate-method 16.76 0.02 16.79
ggplot-method 10.97 0.05 11.02
layout_circle-method 9.61 0.03 9.64
stat_reduce-method 7.49 0.20 7.77
stat_bin-method 7.49 0.03 7.52
stat_slice-method 7.25 0.00 7.25
scale_fill_giemsa 6.63 0.01 6.64
plotGrandLinear 6.25 0.03 6.29
geom_chevron-method 5.87 0.04 5.96
** running examples for arch 'x64' ... [435s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 109.17 0.50 109.73
layout_karyogram-method 43.18 0.07 43.26
tracks 41.99 0.01 42.43
geom_alignment-method 36.33 0.64 36.97
geom_arrow-method 21.67 0.05 22.05
plotRangesLinkedToData 20.20 0.42 20.84
stat_aggregate-method 19.39 0.03 19.45
ggplot-method 14.06 0.02 14.18
layout_circle-method 13.37 0.02 13.39
stat_bin-method 8.69 0.01 8.71
plotGrandLinear 8.54 0.02 8.60
geom_chevron-method 8.44 0.03 8.47
geom_arrowrect-method 6.63 0.09 6.78
stat_reduce-method 6.38 0.22 6.62
scale_fill_giemsa 6.12 0.05 6.16
stat_slice-method 5.74 0.03 5.78
geom_rect-method 5.21 0.03 6.10
stat_identity-method 5.05 0.03 5.08
geom_segment-method 4.90 0.01 5.06
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R' [13s]
[13s] OK
** running tests for arch 'x64' ...
Running 'test-all.R' [18s]
[19s] 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
WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/ggbio.Rcheck/00check.log'
for details.
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 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'
** 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_1.14.0.zip
* DONE (ggbio)