ggbio 1.24.1
Michael Lawrence
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/ggbio | | Branch: RELEASE_3_5 | | Last Commit: ef04c1b | | Last Changed Date: 2017-06-23 13:52:53 -0400 (Fri, 23 Jun 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf ggbio.buildbin-libdir ggbio.Rcheck && mkdir ggbio.buildbin-libdir ggbio.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.24.1.tar.gz >ggbio.Rcheck\00install.out 2>&1 && cp ggbio.Rcheck\00install.out ggbio-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.24.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ggbio.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.24.1'
* 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 ... OK
* 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:
'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion'
'ggplot2:::rename_aes' '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
.combineNames: no visible binding for global variable
'.layout_circle.stats'
Ideogram: no visible global function definition for 'data'
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: no visible binding for global variable
'variable'
autoplot,RangedSummarizedExperiment: no visible binding for global
variable 'variable'
autoplot,VCF: no visible binding for global variable 'stepping'
autoplot,VCF: no visible binding for global variable 'value'
autoplot,VRanges: no visible binding for global variable 'midpoint'
autoplot,Views: no visible binding for global variable 'x'
autoplot,Views: no visible binding for global variable 'value'
geom_alignment,BamFile: no visible binding for global variable 'fl'
geom_alignment,BamFile: no visible binding for global variable
'stepping'
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: no visible binding for global variable
'gieStain'
layout_karyogram,GRanges: no visible binding for global variable 'x'
layout_karyogram,GRanges: no visible binding for global variable 'y'
layout_karyogram,GRanges: no visible binding for global variable 'xend'
layout_karyogram,GRanges: no visible binding for global variable 'yend'
layout_karyogram,GRanges: no visible binding for global variable 'y2'
layout_karyogram,GRanges: no visible binding for global variable
'yend2'
layout_karyogram,GRanges : <anonymous>: no visible binding for global
variable 'name'
layout_karyogram,GRanges : <anonymous>: no visible binding for global
variable 'gieStain'
plotFragLength,character-GRanges: no visible binding for global
variable '.fragLength'
plotSpliceSum,character-EnsDb: possible error in GRangesFilter(which,
condition = "overlapping"): unused argument (condition =
"overlapping")
stat_mismatch,GRanges: no visible binding for global variable 'sts'
stat_mismatch,GRanges: no visible binding for global variable 'eds'
stat_mismatch,GRanges: no visible binding for global variable 'read'
Undefined global functions or variables:
.fragLength .layout_circle.stats .x breaks coefs cytobands data eds
fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se
stepping sts value variable x xend y y.text y2 yend yend2
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 92.45 1.15 95.94
geom_alignment-method 37.77 0.46 44.06
tracks 31.61 0.11 31.78
layout_karyogram-method 26.89 0.00 27.25
stat_reduce-method 10.95 0.09 11.04
plotRangesLinkedToData 10.90 0.11 11.01
ggplot-method 9.69 0.11 17.42
stat_aggregate-method 7.67 0.00 7.67
geom_arrow-method 7.20 0.01 7.22
stat_bin-method 5.81 0.00 5.81
plotGrandLinear 5.49 0.06 5.83
layout_circle-method 5.42 0.03 7.19
geom_rect-method 2.91 0.02 7.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 101.39 0.79 103.61
geom_alignment-method 37.69 0.46 38.15
tracks 35.70 0.05 35.75
layout_karyogram-method 29.84 0.06 29.91
plotRangesLinkedToData 14.56 0.12 14.68
geom_arrow-method 13.36 0.02 13.38
stat_aggregate-method 9.98 0.02 10.00
ggplot-method 9.75 0.08 9.83
stat_reduce-method 8.98 0.11 9.10
stat_bin-method 7.08 0.01 7.09
layout_circle-method 7.02 0.00 7.02
plotGrandLinear 6.60 0.02 6.61
arrangeGrobByParsingLegend 5.45 0.00 5.46
geom_chevron-method 5.37 0.03 5.41
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
Running 'test-all.R'
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 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-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 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_1.24.1.zip
* DONE (ggbio)