Michael Lawrence
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ggbio |
| Branch: RELEASE_3_6 |
| Last Commit: b4f4c89 |
| Last Changed Date: 2018-03-08 07:47:27 -0400 (Thu, 08 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:21:20 -0400 (Thu, 12 Apr 2018).
| Package 582/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggbio 1.26.1 Michael Lawrence
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ggbio |
| Version: 1.26.1 |
| Command: rm -rf ggbio.buildbin-libdir ggbio.Rcheck && mkdir ggbio.buildbin-libdir ggbio.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.26.1.tar.gz >ggbio.Rcheck\00install.out 2>&1 && cp ggbio.Rcheck\00install.out ggbio-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.26.1.tar.gz |
| StartedAt: 2018-04-12 00:23:49 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:42:37 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 1127.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ggbio.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### rm -rf ggbio.buildbin-libdir ggbio.Rcheck && mkdir ggbio.buildbin-libdir ggbio.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.26.1.tar.gz >ggbio.Rcheck\00install.out 2>&1 && cp ggbio.Rcheck\00install.out ggbio-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.26.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ggbio.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.26.1'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_aggregate-method.Rd:48: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:45: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:48: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:51: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:54: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:64: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:66: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:69: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:72: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:75: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:78: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:85: missing file link 'slice'
See 'C:/Users/biocbuild/bbs-3.6-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:
'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: no visible binding for global variable 'name'
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 104.30 1.20 105.85
geom_alignment-method 39.50 0.39 39.89
tracks 33.32 0.05 33.37
layout_karyogram-method 22.92 0.05 22.98
plotRangesLinkedToData 11.67 0.18 11.85
stat_reduce-method 9.87 0.32 10.18
ggplot-method 9.59 0.10 9.74
geom_arrow-method 8.64 0.03 8.67
stat_aggregate-method 8.35 0.03 8.38
stat_bin-method 6.01 0.03 6.04
layout_circle-method 5.72 0.03 5.75
plotGrandLinear 5.50 0.04 5.54
arrangeGrobByParsingLegend 5.08 0.05 5.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 105.34 1.12 106.84
tracks 48.91 0.10 49.02
geom_alignment-method 40.08 0.44 40.51
layout_karyogram-method 38.90 0.05 38.96
plotRangesLinkedToData 17.00 0.08 17.07
stat_aggregate-method 15.09 0.00 15.10
geom_arrow-method 14.20 0.03 14.23
stat_reduce-method 10.12 0.13 10.25
plotGrandLinear 9.14 0.04 9.19
stat_bin-method 9.08 0.00 9.08
ggplot-method 8.39 0.01 8.40
layout_circle-method 7.03 0.02 7.04
arrangeGrobByParsingLegend 5.61 0.02 5.63
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-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 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
converting help for package 'ggbio'
finding HTML links ... done
Grob-class html
Plot-class html
Tracked-class html
arrangeGrobByParsingLegend html
autoplot-method html
finding level-2 HTML links ... done
geom_alignment-method html
geom_arch-method html
geom_arrow-method html
geom_arrowrect-method html
geom_bar-method html
geom_chevron-method html
geom_rect-method html
geom_segment-method html
ggbio-class html
ggplot-method html
ggsave html
layout_circle-method html
layout_karyogram-method html
nav html
plotFragLength html
plotGrandLinear html
plotRangesLinkedToData html
plotSingleChrom html
plotSpliceSum html
plotStackedOverview html
rescale-method html
scale_fill_fold_change html
scale_fill_giemsa html
scale_x_sequnit html
stat_aggregate-method html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_aggregate-method.Rd:48: missing file link 'findOverlaps'
stat_bin-method html
stat_coverage-method html
stat_gene-method html
stat_identity-method html
stat_mismatch-method html
stat_reduce-method html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:45: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:48: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:51: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:54: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_reduce-method.Rd:64: missing file link 'reduce'
stat_slice-method html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:66: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:69: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:72: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:75: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:78: missing file link 'slice'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEB9N4k/R.INSTALL24a42feb2e1d/ggbio/man/stat_slice-method.Rd:85: missing file link 'slice'
stat_stepping-method html
stat_table-method html
theme html
tracks html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ggbio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggbio' as ggbio_1.26.1.zip
* DONE (ggbio)
In R CMD INSTALL
In R CMD INSTALL
|
ggbio.Rcheck/tests_i386/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> test_check("ggbio")
Loading required package: ggbio
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
== testthat results ===========================================================
OK: 0 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
9.73 0.46 10.28
|
ggbio.Rcheck/tests_x64/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> test_check("ggbio")
Loading required package: ggbio
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
== testthat results ===========================================================
OK: 0 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
12.67 0.42 35.12
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ggbio.Rcheck/examples_i386/ggbio-Ex.timings
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ggbio.Rcheck/examples_x64/ggbio-Ex.timings
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