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 10:29:58 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GoogleGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GoogleGenomics_2.3.2.tar.gz |
| StartedAt: 2018-10-29 03:43:46 -0400 (Mon, 29 Oct 2018) |
| EndedAt: 2018-10-29 03:53:52 -0400 (Mon, 29 Oct 2018) |
| EllapsedTime: 605.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GoogleGenomics.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GoogleGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GoogleGenomics_2.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GoogleGenomics.Rcheck' * using R Under development (unstable) (2018-10-22 r75479) * 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 '2.3.2' * 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 whether package 'GoogleGenomics' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/GoogleGenomics/man/variantsToVRanges.Rd:18: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic Warning: Package 'GoogleGenomics' is deprecated and will be removed from See 'C:/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 * 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-3.9-bioc/R/library/GoogleGenomics/libs/i386/GoogleGenomics.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GoogleGenomics/libs/x64/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-3.9-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/3.9/bioc/src/contrib/GoogleGenomics_2.3.2.tar.gz && rm -rf GoogleGenomics.buildbin-libdir && mkdir GoogleGenomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GoogleGenomics.buildbin-libdir GoogleGenomics_2.3.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GoogleGenomics_2.3.2.zip && rm GoogleGenomics_2.3.2.tar.gz GoogleGenomics_2.3.2.zip
###
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install for i386
* installing *source* package 'GoogleGenomics' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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-3.9-bioc/tmpdir/Rtmpqs7FQs/R.INSTALL17c07cf0113c/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.
Warning: Package 'GoogleGenomics' is deprecated and will be removed from
Bioconductor version 3.9
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˜1.9-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˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GoogleGenomics.buildbin-libdir/GoogleGenomics/libs/x64
** 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
* MD5 sums
packaged installation of 'GoogleGenomics' as GoogleGenomics_2.3.2.zip
* DONE (GoogleGenomics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GoogleGenomics' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GoogleGenomics.Rcheck/tests_i386/runTests.Rout
R Under development (unstable) (2018-10-22 r75479) -- "Unsuffered Consequences"
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, 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: 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
63.57 3.15 86.32
|
GoogleGenomics.Rcheck/tests_x64/runTests.Rout
R Under development (unstable) (2018-10-22 r75479) -- "Unsuffered Consequences"
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, 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: 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
76.70 2.25 98.76
|
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GoogleGenomics.Rcheck/examples_i386/GoogleGenomics-Ex.timings
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GoogleGenomics.Rcheck/examples_x64/GoogleGenomics-Ex.timings
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