Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:27:31 -0400 (Tue, 09 Apr 2019).
Package 636/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
geneXtendeR 1.9.0 Bohdan Khomtchouk
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: geneXtendeR |
Version: 1.9.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneXtendeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings geneXtendeR_1.9.0.tar.gz |
StartedAt: 2019-04-09 02:59:15 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 03:36:19 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 2224.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: geneXtendeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneXtendeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings geneXtendeR_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/geneXtendeR.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'geneXtendeR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'geneXtendeR' version '1.9.0' * package encoding: UTF-8 * 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 'geneXtendeR' can be installed ... OK * checking installed package size ... NOTE installed size is 11.6Mb sub-directories of 1Mb or more: data 5.8Mb doc 1.9Mb extdata 3.5Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: 'rtracklayer' A package should be listed in only one of these fields. * 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 Namespaces in Imports field not imported from: 'BiocStyle' 'SnowballC' 'org.Rn.eg.db' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .geneXtender: no visible binding for global variable 'type' .geneXtender: no visible binding for global variable 'seqid' .geneXtender: no visible binding for global variable 'gene_id' .geneXtender: no visible binding for global variable 'gene_name' annotate_n: no visible binding for global variable '..I' annotate_n: no visible binding for global variable 'seqid' diffGO: no visible binding for global variable 'rat' gene_annotate: no visible global function definition for '.' gene_annotate: no visible binding for global variable 'Distance-of-Gene-to-Nearest-Peak' gene_annotate: no visible global function definition for 'sd' gene_annotate: no visible binding for global variable 'Chromosome' gene_annotate: no visible binding for global variable 'Gene-Start' gene_annotate: no visible binding for global variable 'Gene-End' gene_annotate: no visible binding for global variable 'Gene-ID' gene_annotate: no visible binding for global variable 'Gene-Name' gene_annotate: no visible binding for global variable 'Peaks-on-Gene-Body' gene_annotate: no visible binding for global variable 'Number-of-Peaks-Associated-with-Gene' gene_lookup: no visible binding for global variable 'gene_name_id' gene_lookup: no visible binding for global variable 'gene_id' gene_lookup : internal_find: no visible binding for global variable 'Chromosome' gene_lookup : internal_find: no visible binding for global variable 'distance' gene_lookup : internal_find: no visible global function definition for 'na.omit' gene_lookup: no visible binding for global variable '..I' gene_lookup: no visible binding for global variable 'distance' makeWordCloud: no visible binding for global variable 'rat' meanPeakLength: no visible binding for global variable 'rat' peaksInput: no visible binding for global variable 'chr' peaksInput: no visible global function definition for 'na.omit' peaksMerge: no visible binding for global variable 'chr' peaksMerge: no visible binding for global variable 'g' peaksMerge: no visible global function definition for '.' plotWordFreq : geneXtender: no visible binding for global variable 'type' plotWordFreq : geneXtender: no visible binding for global variable 'seqid' plotWordFreq : geneXtender: no visible binding for global variable 'gene_id' plotWordFreq : geneXtender: no visible binding for global variable 'gene_name' Undefined global functions or variables: . ..I Chromosome Distance-of-Gene-to-Nearest-Peak Gene-End Gene-ID Gene-Name Gene-Start Number-of-Peaks-Associated-with-Gene Peaks-on-Gene-Body chr distance g gene_id gene_name gene_name_id na.omit rat sd seqid type Consider adding importFrom("stats", "na.omit", "sd") 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/geneXtendeR/libs/i386/geneXtendeR.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/geneXtendeR/libs/x64/geneXtendeR.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... NOTE Files named as vignettes but with no recognized vignette engine: 'vignettes/geneXtendeR.Rnw' (Is a VignetteBuilder field missing?) * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed meanPeakLengthPlot 48.70 1.39 56.11 cumlinePlot 41.42 1.18 46.28 hotspotPlot 40.31 0.89 192.13 gene_annotate 34.39 0.48 39.32 barChart 30.89 0.70 34.68 diffGO 28.70 0.81 37.57 annotate 26.16 0.91 29.97 linePlot 26.05 0.44 42.18 distinct 23.30 0.39 27.04 plotWordFreq 21.57 0.36 26.19 makeWordCloud 20.66 0.48 174.75 makeNetwork 18.78 0.56 40.43 gene_lookup 18.98 0.27 21.86 peakLengthBoxplot 18.28 0.44 21.47 meanPeakLength 16.47 0.35 21.10 peaksInput 0.59 0.12 9.28 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed meanPeakLengthPlot 44.81 0.74 51.21 hotspotPlot 37.73 0.84 41.42 cumlinePlot 29.06 0.75 32.55 linePlot 28.64 0.48 31.64 barChart 27.27 0.65 34.28 annotate 22.71 0.60 25.75 gene_annotate 21.77 0.54 24.92 makeWordCloud 21.25 0.68 24.78 diffGO 19.47 0.53 22.55 gene_lookup 19.08 0.32 22.36 plotWordFreq 18.91 0.42 21.62 makeNetwork 18.64 0.46 24.07 peakLengthBoxplot 16.82 0.54 20.14 meanPeakLength 16.34 0.36 19.89 distinct 16.37 0.29 18.98 * 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 PDF version of manual ... OK * DONE Status: 6 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/geneXtendeR.Rcheck/00check.log' for details.
geneXtendeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/geneXtendeR_1.9.0.tar.gz && rm -rf geneXtendeR.buildbin-libdir && mkdir geneXtendeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneXtendeR.buildbin-libdir geneXtendeR_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL geneXtendeR_1.9.0.zip && rm geneXtendeR_1.9.0.tar.gz geneXtendeR_1.9.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 11.7M 100 11.7M 0 0 53.7M 0 --:--:-- --:--:-- --:--:-- 55.7M install for i386 * installing *source* package 'geneXtendeR' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c annotate.c -o annotate.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c extract_number.c -o extract_number.o extract_number.c: In function 'extractnumber': extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable] long n_1; ^ extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable] long j_1; ^ extract_number.c:54:12: warning: variable 'pvcfcol5_5' set but not used [-Wunused-but-set-variable] char * pvcfcol5_5; ^ extract_number.c:53:12: warning: variable 'pvcfcol4_4' set but not used [-Wunused-but-set-variable] char * pvcfcol4_4; ^ extract_number.c:52:12: warning: variable 'pvcfcol3_3' set but not used [-Wunused-but-set-variable] char * pvcfcol3_3; ^ extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable] char * pvcfcol2_2; ^ extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable] char * pvcfcol1_1; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c extract_peaks.c -o extract_peaks.o C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/geneXtendeR.buildbin-libdir/00LOCK-geneXtendeR/00new/geneXtendeR/libs/i386 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'geneXtendeR' finding HTML links ... done allPeakLengths html annotate html annotate_n html barChart html cumlinePlot html diffGO html distinct html dot-geneXtender html gene_annotate html gene_lookup html hotspotPlot html linePlot html makeNetwork html makeWordCloud html meanPeakLength html meanPeakLengthPlot html peakLengthBoxplot html peaksInput html peaksMerge html plotWordFreq html rat html samplepeaksinput 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 'geneXtendeR' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c annotate.c -o annotate.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c extract_number.c -o extract_number.o extract_number.c: In function 'extractnumber': extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable] long n_1; ^ extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable] long j_1; ^ extract_number.c:54:12: warning: variable 'pvcfcol5_5' set but not used [-Wunused-but-set-variable] char * pvcfcol5_5; ^ extract_number.c:53:12: warning: variable 'pvcfcol4_4' set but not used [-Wunused-but-set-variable] char * pvcfcol4_4; ^ extract_number.c:52:12: warning: variable 'pvcfcol3_3' set but not used [-Wunused-but-set-variable] char * pvcfcol3_3; ^ extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable] char * pvcfcol2_2; ^ extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable] char * pvcfcol1_1; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c extract_peaks.c -o extract_peaks.o C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/geneXtendeR.buildbin-libdir/geneXtendeR/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'geneXtendeR' as geneXtendeR_1.9.0.zip * DONE (geneXtendeR) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'geneXtendeR' successfully unpacked and MD5 sums checked
geneXtendeR.Rcheck/tests_i386/testthat.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 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(geneXtendeR) Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: stats4 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, 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 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: GenomeInfoDb Loading required package: GO.db 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")'. > > test_check("geneXtendeR") == testthat results =========================================================== OK: 86 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 269.73 110.01 366.20 |
geneXtendeR.Rcheck/tests_x64/testthat.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 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(geneXtendeR) Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: stats4 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, 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 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: GenomeInfoDb Loading required package: GO.db 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")'. > > test_check("geneXtendeR") == testthat results =========================================================== OK: 86 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 240.60 44.39 289.45 |
geneXtendeR.Rcheck/examples_i386/geneXtendeR-Ex.timings
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geneXtendeR.Rcheck/examples_x64/geneXtendeR-Ex.timings
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