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CHECK report for GoogleGenomics on merida2

This page was generated on 2018-10-29 10:46:47 -0400 (Mon, 29 Oct 2018).

Package 660/1642HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GoogleGenomics 2.3.2
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)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GoogleGenomics
Version: 2.3.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GoogleGenomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GoogleGenomics_2.3.2.tar.gz
StartedAt: 2018-10-29 01:25:01 -0400 (Mon, 29 Oct 2018)
EndedAt: 2018-10-29 01:30:18 -0400 (Mon, 29 Oct 2018)
EllapsedTime: 317.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GoogleGenomics.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GoogleGenomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GoogleGenomics_2.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GoogleGenomics.Rcheck’
* using R Under development (unstable) (2018-04-05 r74542)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘/Users/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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/GoogleGenomics.Rcheck/00check.log’
for details.



Installation output

GoogleGenomics.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GoogleGenomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GoogleGenomics’ ...
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 clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking for pkg-config... 0
checking if ProtoBuf version >= 3.0.0... "yes"
checking for protoc... /usr/local/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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I.  -I/usr/local/include   -fPIC  -Wall -g -O2 -c init.cc -o init.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GoogleGenomics.so init.o -L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output

GoogleGenomics.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-04-05 r74542) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 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 
 45.182   1.477  66.788 

Example timings

GoogleGenomics.Rcheck/GoogleGenomics-Ex.timings

nameusersystemelapsed
authenticate0.0060.0000.006
callGRPCMethod0.0010.0010.002
defaultGcloudCredsPath0.0010.0000.001
getRProtoBufDefaultObject0.0010.0010.002
getReads0.0900.0140.515
getReadsPage0.0230.0010.217
getSearchPage0.0260.0010.215
getVariantCalls0.0010.0000.001
getVariants0.2680.0160.769
getVariantsPage0.2850.0210.818
readsToGAlignments0.2660.0060.674
variantsToGRanges1.6110.0562.712
variantsToVRanges1.5590.1522.745