Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:27:29 -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: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GoogleGenomics.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GoogleGenomics_2.2.0.tar.gz |
StartedAt: 2018-10-16 00:54:18 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 00:58:03 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 225.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GoogleGenomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GoogleGenomics.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GoogleGenomics_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/GoogleGenomics.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * 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 for sufficient/correct file permissions ... OK * checking whether package ‘GoogleGenomics’ 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 * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/GoogleGenomics.Rcheck/00check.log’ for details.
GoogleGenomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL GoogleGenomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘GoogleGenomics’ ... /home/biocbuild/bbs-3.7-bioc/R/bin/Rcmd: 62: exec: CONFIG: not found checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for pkg-config... 0 checking if ProtoBuf version >= 3.0.0... "no" configure: WARNING: " gRPC installation could not be found, or protocol buffer library is not >= 3.0.0. If your installation is in a non-standard location, please see installation instructions at https://github.com/Bioconductor/GoogleGenomics/blob/master/README.rst " configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -I. -I/usr/local/include -fpic -g -O2 -c init.cc -o init.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o GoogleGenomics.so init.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/GoogleGenomics/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Configured public API key. * DONE (GoogleGenomics)
GoogleGenomics.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 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 25.444 0.432 47.526
GoogleGenomics.Rcheck/GoogleGenomics-Ex.timings
name | user | system | elapsed | |
authenticate | 0.076 | 0.000 | 0.073 | |
callGRPCMethod | 0.000 | 0.000 | 0.001 | |
defaultGcloudCredsPath | 0 | 0 | 0 | |
getRProtoBufDefaultObject | 0.000 | 0.000 | 0.001 | |
getReads | 0.160 | 0.004 | 1.163 | |
getReadsPage | 0.024 | 0.004 | 0.838 | |
getSearchPage | 0.028 | 0.000 | 0.390 | |
getVariantCalls | 0.004 | 0.000 | 0.001 | |
getVariants | 0.224 | 0.016 | 0.834 | |
getVariantsPage | 0.164 | 0.008 | 0.839 | |
readsToGAlignments | 0.204 | 0.000 | 0.719 | |
variantsToGRanges | 1.352 | 0.008 | 2.688 | |
variantsToVRanges | 0.856 | 0.076 | 2.318 | |