Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:31:29 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the ggbio package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 736/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggbio 1.38.0 (landing page) Michael Lawrence
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ggbio |
Version: 1.38.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ggbio_1.38.0.tar.gz |
StartedAt: 2021-05-06 03:11:21 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 03:30:34 -0400 (Thu, 06 May 2021) |
EllapsedTime: 1153.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ggbio.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ggbio_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ggbio.Rcheck' * using R version 4.0.5 (2021-03-31) * 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 '1.38.0' * 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: Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_aggregate-method.Rd:48: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:45: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:48: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:51: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:54: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:64: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:66: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:69: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:72: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:75: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:78: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:85: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.12-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 ':::' call which should be '::': 'ggplot2:::set_last_plot' See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: 'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion' 'ggplot2:::rename_aes' 'ggplot2:::rescale01' 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' 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' 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 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 include directives in Makefiles ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed autoplot-method 126.71 2.90 136.29 geom_alignment-method 46.04 0.52 46.58 tracks 20.68 0.01 20.77 layout_karyogram-method 20.05 0.13 20.17 plotRangesLinkedToData 12.21 0.18 12.39 stat_reduce-method 11.72 0.09 11.81 ggplot-method 11.61 0.05 11.66 stat_aggregate-method 9.92 0.02 9.93 plotGrandLinear 8.45 0.09 8.55 layout_circle-method 7.93 0.04 7.98 stat_bin-method 5.45 0.02 5.47 geom_arrow-method 5.36 0.01 5.37 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed autoplot-method 89.40 0.99 90.50 geom_alignment-method 35.08 0.47 35.76 tracks 20.19 0.05 20.24 layout_karyogram-method 15.18 0.06 15.27 plotRangesLinkedToData 9.99 0.09 10.07 stat_aggregate-method 9.69 0.03 9.72 stat_reduce-method 7.51 0.08 7.59 ggplot-method 7.27 0.02 7.28 layout_circle-method 6.25 0.00 6.25 plotGrandLinear 5.98 0.05 6.04 geom_arrow-method 5.28 0.00 5.28 * 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-3.12-bioc/meat/ggbio.Rcheck/00check.log' for details.
ggbio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ggbio_1.38.0.tar.gz && rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggbio.buildbin-libdir ggbio_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ggbio_1.38.0.zip && rm ggbio_1.38.0.tar.gz ggbio_1.38.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 1307k 0 7055 0 0 579k 0 0:00:02 --:--:-- 0:00:02 574k 100 1307k 100 1307k 0 0 37.5M 0 --:--:-- --:--:-- --:--:-- 37.5M install for i386 * installing *source* package 'ggbio' ... ** using staged installation ** R ** inst ** byte-compile and prepare 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-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_aggregate-method.Rd:48: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic 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-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:45: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:48: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:51: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:54: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_reduce-method.Rd:64: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic stat_slice-method html Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:66: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:69: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:72: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:75: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:78: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkhUGPi/R.INSTALL1f0443725501/ggbio/man/stat_slice-method.Rd:85: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic stat_stepping-method html stat_table-method html theme html tracks html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'ggbio' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ggbio' as ggbio_1.38.0.zip * DONE (ggbio) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'ggbio' successfully unpacked and MD5 sums checked
ggbio.Rcheck/tests_i386/test-all.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 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, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, 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 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 16.53 1.75 21.31 |
ggbio.Rcheck/tests_x64/test-all.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 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, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, 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 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 21.04 0.71 26.54 |
ggbio.Rcheck/examples_i386/ggbio-Ex.timings
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ggbio.Rcheck/examples_x64/ggbio-Ex.timings
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