Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:40:21 -0400 (Wed, 17 Oct 2018).
Package 629/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GoogleGenomics 2.2.0 Siddhartha Bagaria
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: GoogleGenomics |
Version: 2.2.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GoogleGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GoogleGenomics_2.2.0.tar.gz |
StartedAt: 2018-10-17 02:28:51 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 02:38:12 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 560.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GoogleGenomics.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GoogleGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GoogleGenomics_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GoogleGenomics.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 'GoogleGenomics/DESCRIPTION' ... OK * this is package 'GoogleGenomics' version '2.2.0' * 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 'GoogleGenomics' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/authenticate.Rd:24: file link 'httpuv' in package 'httpuv' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/callGRPCMethod.Rd:15: file link 'RProtoBuf' in package 'RProtoBuf' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/getRProtoBufDefaultObject.Rd:6: file link 'RProtoBuf' in package 'RProtoBuf' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/readsToGAlignments.Rd:18: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/variantsToGRanges.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/variantsToVRanges.Rd:18: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GoogleGenomics.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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.7-bioc/R/library/GoogleGenomics/libs/i386/GoogleGenomics.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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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-3.7-bioc/meat/GoogleGenomics.Rcheck/00check.log' for details.
GoogleGenomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GoogleGenomics_2.2.0.tar.gz && rm -rf GoogleGenomics.buildbin-libdir && mkdir GoogleGenomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GoogleGenomics.buildbin-libdir GoogleGenomics_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GoogleGenomics_2.2.0.zip && rm GoogleGenomics_2.2.0.tar.gz GoogleGenomics_2.2.0.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 101k 100 101k 0 0 1906k 0 --:--:-- --:--:-- --:--:-- 2207k install for i386 * installing *source* package 'GoogleGenomics' ... ** libs C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cc -o init.o C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GoogleGenomics.dll tmp.def init.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GoogleGenomics.buildbin-libdir/GoogleGenomics/libs/i386 ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GoogleGenomics' finding HTML links ... done GoogleGenomics html authenticate html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/authenticate.Rd:24: file link 'httpuv' in package 'httpuv' does not exist and so has been treated as a topic callGRPCMethod html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/callGRPCMethod.Rd:15: file link 'RProtoBuf' in package 'RProtoBuf' does not exist and so has been treated as a topic defaultGcloudCredsPath html getRProtoBufDefaultObject html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/getRProtoBufDefaultObject.Rd:6: file link 'RProtoBuf' in package 'RProtoBuf' does not exist and so has been treated as a topic getReads html getReadsPage html getSearchPage html getVariantCalls html getVariants html getVariantsPage html isGRPCAvailable html readsToGAlignments html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/readsToGAlignments.Rd:18: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic variantsToGRanges html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/variantsToGRanges.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic variantsToVRanges html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQnRXol/R.INSTALL1b3419b330c5/GoogleGenomics/man/variantsToVRanges.Rd:18: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic ** building package indices ** installing vignettes ** testing if installed package can be loaded Configured public API key. In R CMD INSTALL install for x64 * installing *source* package 'GoogleGenomics' ... ** libs C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cc -o init.o C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GoogleGenomics.dll tmp.def init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GoogleGenomics.buildbin-libdir/GoogleGenomics/libs/x64 ** testing if installed package can be loaded Configured public API key. * MD5 sums packaged installation of 'GoogleGenomics' as GoogleGenomics_2.2.0.zip * DONE (GoogleGenomics) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'GoogleGenomics' successfully unpacked and MD5 sums checked In R CMD INSTALL
GoogleGenomics.Rcheck/tests_i386/runTests.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. > # The tests will only be run if there is an environment variable called > # GOOGLE_API_KEY containing the public API key. > > # Get the API key from the environment variable. > if (GoogleGenomics::authenticate()) { + # Perform the tests + library(testthat) + test_check("GoogleGenomics") + message("SUCCESS: All tests pass.") + } else { + # Skip the tests + warning(paste( + "Public key unavailable for authentication with Google Genomics.", + "Skipping tests...")) + } Configured public API key. Configured public API key. Loading required package: GoogleGenomics Loading required package: GenomicAlignments 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: GenomeInfoDb Loading required package: GenomicRanges Loading required package: SummarizedExperiment 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: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: VariantAnnotation Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate == testthat results =========================================================== OK: 26 SKIPPED: 0 FAILED: 0 SUCCESS: All tests pass. > > proc.time() user system elapsed 59.48 3.67 83.85 |
GoogleGenomics.Rcheck/tests_x64/runTests.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. > # The tests will only be run if there is an environment variable called > # GOOGLE_API_KEY containing the public API key. > > # Get the API key from the environment variable. > if (GoogleGenomics::authenticate()) { + # Perform the tests + library(testthat) + test_check("GoogleGenomics") + message("SUCCESS: All tests pass.") + } else { + # Skip the tests + warning(paste( + "Public key unavailable for authentication with Google Genomics.", + "Skipping tests...")) + } Configured public API key. Configured public API key. Loading required package: GoogleGenomics Loading required package: GenomicAlignments 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: GenomeInfoDb Loading required package: GenomicRanges Loading required package: SummarizedExperiment 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: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: VariantAnnotation Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate == testthat results =========================================================== OK: 26 SKIPPED: 0 FAILED: 0 SUCCESS: All tests pass. > > proc.time() user system elapsed 57.18 2.64 80.18 |
GoogleGenomics.Rcheck/examples_i386/GoogleGenomics-Ex.timings
|
GoogleGenomics.Rcheck/examples_x64/GoogleGenomics-Ex.timings
|