ggbio 1.18.5
Tengfei Yin
| 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/ggbio | | Last Changed Rev: 113590 / Revision: 116712 | | Last Changed Date: 2016-02-12 11:55:15 -0800 (Fri, 12 Feb 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### 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_1.18.5.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_1.18.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ggbio.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 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.18.5'
* 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: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
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:
'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion'
'ggplot2:::rescale01' 'ggplot2:::set_last_plot'
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
autoplot,matrix : .local: warning in scale_x_continuous(breaks = x,
label = x.lab, expand = c(0, 0)): partial argument match of 'label'
to 'labels'
autoplot,matrix : .local: warning in scale_x_continuous(breaks = NULL,
label = NULL, expand = c(0, 0)): partial argument match of 'label' to
'labels'
print,Ideogram : .local: warning in scale_y_continuous(breaks = 5,
label = subchr): partial argument match of 'label' to 'labels'
.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'
getNR: no visible global function definition for 'se'
getNR: no visible global function definition for 'indexProbesProcessed'
getNR: no visible global function definition for 'coefs'
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 'variable'
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 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 ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'PlotList,numeric,missing,ANY'
generic '[' and siglist 'Tracks,numeric,missing,ANY'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [409s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 78.31 0.39 144.55
geom_alignment-method 48.01 0.28 48.74
tracks 38.30 0.03 38.68
layout_karyogram-method 23.48 0.01 25.34
plotRangesLinkedToData 13.59 0.17 13.76
stat_aggregate-method 11.89 0.01 11.95
stat_reduce-method 11.78 0.07 11.84
geom_arrow-method 11.81 0.00 12.28
ggplot-method 10.20 0.03 10.56
stat_bin-method 7.52 0.00 7.52
plotGrandLinear 7.24 0.02 7.55
layout_circle-method 7.03 0.02 7.05
stat_slice-method 5.99 0.00 6.03
geom_chevron-method 5.25 0.00 5.26
arrangeGrobByParsingLegend 3.53 0.03 9.72
** running examples for arch 'x64' ... [413s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 95.80 0.58 97.15
geom_alignment-method 51.78 0.23 52.01
tracks 42.49 0.03 46.47
layout_karyogram-method 35.93 0.02 36.02
plotRangesLinkedToData 15.83 0.14 16.44
stat_aggregate-method 14.62 0.00 14.83
geom_arrow-method 14.41 0.03 14.45
ggplot-method 12.71 0.04 13.06
layout_circle-method 11.92 0.03 11.94
stat_reduce-method 10.60 0.04 10.67
stat_bin-method 9.37 0.01 9.57
plotGrandLinear 8.91 0.06 8.97
geom_chevron-method 7.50 0.01 7.52
geom_rect-method 5.60 0.03 5.76
geom_arrowrect-method 5.59 0.00 5.58
stat_identity-method 5.30 0.00 6.01
stat_slice-method 5.14 0.02 6.58
geom_segment-method 5.15 0.00 5.15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R' [14s]
[14s] OK
** running tests for arch 'x64' ...
Running 'test-all.R' [15s]
[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: 2 WARNINGs, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/ggbio.Rcheck/00check.log'
for details.