ggbio 1.17.2
Tengfei Yin
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggbio | | Last Changed Rev: 106491 / Revision: 107602 | | Last Changed Date: 2015-07-16 10:05:21 -0700 (Thu, 16 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 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-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.17.2.tar.gz >ggbio.Rcheck\00install.out 2>&1 && cp ggbio.Rcheck\00install.out ggbio-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.17.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ggbio.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.17.2'
* 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-3.2-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 ... NOTE
Malformed Title field: should not end in a period.
* 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
stat_mismatch,BamFile : .local: warning in pileupAsGRanges(data, region
= which): partial argument match of 'region' to 'regions'
.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'
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'
autoplot,ExpressionSet : .local: no visible binding for global variable
'variable'
autoplot,RangedSummarizedExperiment : .local: no visible binding for
global variable 'sset'
autoplot,RangedSummarizedExperiment : .local: no visible binding for
global variable 'variable'
autoplot,TabixFile : .local: no visible global function definition for
'file_ext'
autoplot,TabixFile : .local: no visible global function definition for
'file_path_sans_ext'
autoplot,TabixFile : .local: no visible global function definition for
'readVcf'
autoplot,VCF : .local: no visible binding for global variable
'stepping'
autoplot,VCF : .local: no visible binding for global variable 'value'
autoplot,VRanges : .local: no visible binding for global variable
'midpoint'
autoplot,Views : .local: no visible binding for global variable 'x'
autoplot,Views : .local: no visible binding for global variable 'value'
geom_alignment,BamFile : .local: no visible binding for global variable
'fl'
geom_alignment,BamFile : .local: no visible binding for global variable
'stepping'
geom_alignment,OrganismDb : .local: no visible global function
definition for 'select'
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'
layout_karyogram,GRanges : .local: no visible binding for global
variable 'gieStain'
layout_karyogram,GRanges : .local: no visible binding for global
variable 'x'
layout_karyogram,GRanges : .local: no visible binding for global
variable 'y'
layout_karyogram,GRanges : .local: no visible binding for global
variable 'xend'
layout_karyogram,GRanges : .local: no visible binding for global
variable 'yend'
layout_karyogram,GRanges : .local: no visible binding for global
variable 'y2'
layout_karyogram,GRanges : .local: no visible binding for global
variable 'yend2'
layout_karyogram,GRanges : .local : <anonymous>: no visible binding for
global variable 'name'
layout_karyogram,GRanges : .local : <anonymous>: no visible binding for
global variable 'gieStain'
plotFragLength,character-GRanges : .local: no visible global function
definition for 'qutoplot'
plotFragLength,character-GRanges : .local: no visible binding for
global variable '.fragLength'
stat_mismatch,GRanges : .local: no visible binding for global variable
'sts'
stat_mismatch,GRanges : .local: no visible binding for global variable
'eds'
stat_mismatch,GRanges : .local: no visible binding for global variable
'read'
* 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 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' ... [338s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 85.81 0.23 90.19
layout_karyogram-method 36.11 0.05 36.35
tracks 34.37 0.01 35.29
geom_alignment-method 26.83 0.03 26.87
plotRangesLinkedToData 15.32 0.19 15.51
geom_arrow-method 14.82 0.03 14.85
stat_aggregate-method 13.20 0.03 13.29
ggplot-method 12.60 0.06 13.00
layout_circle-method 9.10 0.00 9.36
stat_bin-method 7.64 0.03 7.67
plotGrandLinear 6.05 0.03 6.08
stat_reduce-method 5.81 0.03 5.85
geom_chevron-method 5.53 0.03 5.82
** running examples for arch 'x64' ... [396s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 100.28 0.46 101.61
tracks 42.99 0.06 43.09
layout_karyogram-method 42.45 0.08 42.53
geom_alignment-method 29.01 0.06 29.53
plotRangesLinkedToData 18.09 0.24 18.33
geom_arrow-method 18.13 0.00 18.83
stat_aggregate-method 16.75 0.00 16.75
ggplot-method 12.21 0.02 12.38
layout_circle-method 10.09 0.03 10.13
stat_bin-method 8.94 0.04 9.02
plotGrandLinear 7.66 0.04 7.76
stat_reduce-method 6.86 0.01 6.88
geom_chevron-method 6.74 0.03 6.77
scale_fill_giemsa 6.58 0.01 6.60
geom_arrowrect-method 5.66 0.00 5.66
stat_slice-method 5.65 0.00 5.65
geom_rect-method 5.40 0.03 6.06
arrangeGrobByParsingLegend 5.16 0.00 5.17
* 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' [14s]
[15s] 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: 1 WARNING, 3 NOTEs
See
'D:/biocbld/bbs-3.2-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_1.17.2.zip
* DONE (ggbio)