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CHECK report for GoogleGenomics on tokay2

This page was generated on 2018-10-17 08:40:21 -0400 (Wed, 17 Oct 2018).

Package 629/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GoogleGenomics 2.2.0
Siddhartha Bagaria
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GoogleGenomics
Branch: RELEASE_3_7
Last Commit: 65aee17
Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK 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  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
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###
### 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.



Installation output

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

Tests output

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 

Example timings

GoogleGenomics.Rcheck/examples_i386/GoogleGenomics-Ex.timings

nameusersystemelapsed
authenticate2.080.342.42
callGRPCMethod000
defaultGcloudCredsPath000
getRProtoBufDefaultObject000
getReads0.090.050.61
getReadsPage0.020.000.28
getSearchPage0.030.020.29
getVariantCalls000
getVariants1.420.012.03
getVariantsPage1.100.061.72
readsToGAlignments0.240.080.80
variantsToGRanges1.980.243.34
variantsToVRanges2.220.123.52

GoogleGenomics.Rcheck/examples_x64/GoogleGenomics-Ex.timings

nameusersystemelapsed
authenticate1.760.532.29
callGRPCMethod000
defaultGcloudCredsPath000
getRProtoBufDefaultObject000
getReads0.080.030.65
getReadsPage0.050.000.28
getSearchPage0.050.000.26
getVariantCalls000
getVariants1.030.001.56
getVariantsPage1.080.021.75
readsToGAlignments0.390.000.88
variantsToGRanges3.040.014.19
variantsToVRanges3.090.144.38