Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:43:14 -0400 (Wed, 17 Oct 2018).
Package 226/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
chimeraviz 1.6.2 Stian Lågstad
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: chimeraviz |
Version: 1.6.2 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings chimeraviz_1.6.2.tar.gz |
StartedAt: 2018-10-17 01:03:35 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 01:17:56 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 861.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chimeraviz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings chimeraviz_1.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/chimeraviz.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'chimeraviz/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'chimeraviz' version '1.6.2' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biostrings' 'GenomicRanges' 'IRanges' 'Gviz' 'S4Vectors' 'ensembldb' 'AnnotationFilter' 'data.table' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'chimeraviz' 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plot_fusion_transcript_with_protein_domain: no visible binding for global variable 'protein_domain_location' Undefined global functions or variables: protein_domain_location * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed plot_fusion 22.59 0.80 23.67 plot_transcripts 15.34 0.66 16.06 plot_fusion_transcript 10.82 0.06 10.89 plot_fusion_transcripts_graph 10.24 0.04 10.28 plot_fusion_transcript_with_protein_domain 8.97 0.07 9.03 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed plot_fusion 31.61 0.71 32.35 plot_transcripts 16.75 0.34 17.09 plot_fusion_transcript 14.41 0.11 14.51 plot_fusion_transcripts_graph 12.41 0.07 12.49 plot_fusion_transcript_with_protein_domain 10.20 0.04 10.25 get_transcripts_ensembl_db 7.49 0.06 7.55 select_transcript 6.15 0.02 6.17 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.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-3.7-bioc/meat/chimeraviz.Rcheck/00check.log' for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/chimeraviz_1.6.2.tar.gz && rm -rf chimeraviz.buildbin-libdir && mkdir chimeraviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chimeraviz.buildbin-libdir chimeraviz_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL chimeraviz_1.6.2.zip && rm chimeraviz_1.6.2.tar.gz chimeraviz_1.6.2.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2463k 100 2463k 0 0 29.4M 0 --:--:-- --:--:-- --:--:-- 32.0M install for i386 * installing *source* package 'chimeraviz' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'chimeraviz' finding HTML links ... done Fusion-class html PartnerGene-class html add_fusion_reads_alignment html chimeraviz-internals-fusions_to_gene_label_data html chimeraviz-internals-fusions_to_link_data html chimeraviz-internals-scaleListToInterval html chimeraviz html create_fusion_report html decide_transcript_category html down_shift html downstream_partner_gene html fetch_reads_from_fastq html fusion_spanning_reads_count html fusion_split_reads_count html fusion_to_data_frame html get_ensembl_ids html get_fusion_by_chromosome html get_fusion_by_gene_name html get_fusion_by_id html get_transcripts_ensembl_db html import_defuse html import_ericscript html import_function_non_ucsc html import_fusioncatcher html import_fusionmap html import_infusion html import_jaffa html import_prada html import_soapfuse html import_starfusion html partner_gene_ensembl_id html partner_gene_junction_sequence html plot_circle html plot_fusion html plot_fusion_reads html plot_fusion_transcript html plot_fusion_transcript_with_protein_domain html plot_fusion_transcripts_graph html plot_transcripts html raw_Homo_sapiens.GRCh37.74 html raw_cytobandhg19 html raw_cytobandhg38 html raw_defuse html raw_ericscript html raw_fusion5267proteindomains html raw_fusion5267reads html raw_fusion5267readsBedGraph html raw_fusioncatcher html raw_fusionmap html raw_infusion html raw_jaffa html raw_prada html raw_soapfuse html raw_starfusion html select_transcript html show-Fusion-method html show-PartnerGene-method html split_on_utr_and_add_feature html upstream_partner_gene html write_fusion_reference html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'chimeraviz' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'chimeraviz' as chimeraviz_1.6.2.zip * DONE (chimeraviz) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'chimeraviz' successfully unpacked and MD5 sums checked In R CMD INSTALL
chimeraviz.Rcheck/tests_i386/testthat.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" 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) > library(chimeraviz) Loading required package: Biostrings 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, colMeans, colSums, colnames, dirname, 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: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid Loading required package: ensembldb Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: AnnotationFilter Attaching package: 'AnnotationFilter' The following object is masked from 'package:Gviz': feature The following object is masked from 'package:testthat': not Attaching package: 'ensembldb' The following object is masked from 'package:stats': filter Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:GenomicRanges': shift The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second > > test_check("chimeraviz") == testthat results =========================================================== OK: 144 SKIPPED: 2 FAILED: 0 Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 111.43 4.67 118.40 |
chimeraviz.Rcheck/tests_x64/testthat.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" 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) > library(chimeraviz) Loading required package: Biostrings 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, colMeans, colSums, colnames, dirname, 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: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid Loading required package: ensembldb Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: AnnotationFilter Attaching package: 'AnnotationFilter' The following object is masked from 'package:Gviz': feature The following object is masked from 'package:testthat': not Attaching package: 'ensembldb' The following object is masked from 'package:stats': filter Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:GenomicRanges': shift The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second > > test_check("chimeraviz") == testthat results =========================================================== OK: 144 SKIPPED: 2 FAILED: 0 Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 119.21 3.25 123.68 |
chimeraviz.Rcheck/examples_i386/chimeraviz-Ex.timings
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chimeraviz.Rcheck/examples_x64/chimeraviz-Ex.timings
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