Siddhartha Bagaria
| Snapshot Date: 2018-10-28 16:46:29 -0400 (Sun, 28 Oct 2018) |
| URL: https://git.bioconductor.org/packages/GoogleGenomics |
| Branch: master |
| Last Commit: f58dcd3 |
| Last Changed Date: 2018-08-03 09:09:20 -0400 (Fri, 03 Aug 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2018-10-29 10:12:53 -0400 (Mon, 29 Oct 2018).
| Package 660/1642 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Siddhartha Bagaria
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: GoogleGenomics |
| Version: 2.3.2 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GoogleGenomics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GoogleGenomics_2.3.2.tar.gz |
| StartedAt: 2018-10-29 03:38:11 -0400 (Mon, 29 Oct 2018) |
| EndedAt: 2018-10-29 03:42:54 -0400 (Mon, 29 Oct 2018) |
| EllapsedTime: 282.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GoogleGenomics.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GoogleGenomics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GoogleGenomics_2.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GoogleGenomics.Rcheck’ * using R Under development (unstable) (2018-10-16 r75448) * 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 ‘2.3.2’ * 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 ... WARNING Found the following significant warnings: Warning: Package 'GoogleGenomics' is deprecated and will be removed from See ‘/home/biocbuild/bbs-3.9-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 * 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/GoogleGenomics.Rcheck/00check.log’ for details.
GoogleGenomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GoogleGenomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘GoogleGenomics’ ... /home/biocbuild/bbs-3.9-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++ -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... g++ -std=gnu++11 -E checking for pkg-config... 0 checking if ProtoBuf version >= 3.0.0... "yes" checking for protoc... /usr/bin/protoc checking gRPC... "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-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o GoogleGenomics.so init.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-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. Warning: Package 'GoogleGenomics' is deprecated and will be removed from Bioconductor version 3.9 * DONE (GoogleGenomics)
GoogleGenomics.Rcheck/tests/runTests.Rout
R Under development (unstable) (2018-10-16 r75448) -- "Unsuffered Consequences"
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, 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: 49 SKIPPED: 0 FAILED: 0
SUCCESS: All tests pass.
Warning message:
Package 'GoogleGenomics' is deprecated and will be removed from
Bioconductor version 3.9
>
> proc.time()
user system elapsed
33.657 0.580 54.082
GoogleGenomics.Rcheck/GoogleGenomics-Ex.timings
| name | user | system | elapsed | |
| authenticate | 0.159 | 0.003 | 0.162 | |
| callGRPCMethod | 0.000 | 0.000 | 0.001 | |
| defaultGcloudCredsPath | 0 | 0 | 0 | |
| getRProtoBufDefaultObject | 0 | 0 | 0 | |
| getReads | 0.189 | 0.003 | 0.992 | |
| getReadsPage | 0.037 | 0.000 | 0.282 | |
| getSearchPage | 0.031 | 0.000 | 0.249 | |
| getVariantCalls | 0 | 0 | 0 | |
| getVariants | 0.217 | 0.013 | 0.804 | |
| getVariantsPage | 0.187 | 0.004 | 0.748 | |
| readsToGAlignments | 0.351 | 0.004 | 0.796 | |
| variantsToGRanges | 1.417 | 0.016 | 3.049 | |
| variantsToVRanges | 1.044 | 0.039 | 2.199 | |