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This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the GA4GHclient package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GA4GHclient.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 682/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GA4GHclient 1.16.0 (landing page) Welliton Souza
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GA4GHclient |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GA4GHclient.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GA4GHclient_1.16.0.tar.gz |
| StartedAt: 2021-10-14 23:21:03 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:26:53 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 349.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GA4GHclient.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GA4GHclient.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GA4GHclient_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GA4GHclient.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GA4GHclient/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GA4GHclient' version '1.16.0' * 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 'GA4GHclient' 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 * 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 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 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.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: OK
GA4GHclient.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GA4GHclient_1.16.0.tar.gz && rm -rf GA4GHclient.buildbin-libdir && mkdir GA4GHclient.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GA4GHclient.buildbin-libdir GA4GHclient_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GA4GHclient_1.16.0.zip && rm GA4GHclient_1.16.0.tar.gz GA4GHclient_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
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install for i386
* installing *source* package 'GA4GHclient' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient'
** help
*** installing help indices
converting help for package 'GA4GHclient'
finding HTML links ... done
GA4GHclient-package html
HGVSnames html
getBiosample html
finding level-2 HTML links ... done
getCallSet html
getDataset html
getExpressionLevel html
getFeature html
getFeatureSet html
getIndividual html
getReadGroupSet html
getReference html
getReferenceSet html
getRnaQuantification html
getRnaQuantificationSet html
getVariant html
getVariantAnnotationSet html
getVariantSet html
listReferenceBases html
makeVCFFromGA4GHResponse html
makeVCFHeaderFromGA4GHResponse html
searchBiosamples html
searchCallSets html
searchDatasets html
searchExpressionLevels html
searchFeatureSets html
searchFeatures html
searchIndividuals html
searchPhenotypeAssociationSets html
searchPhenotypeAssociations html
searchReadGroupSets html
searchReads html
searchReferenceSets html
searchReferences html
searchRnaQuantificationSets html
searchRnaQuantifications html
searchVariantAnnotationSets html
searchVariantAnnotations html
searchVariantSets html
searchVariants html
searchVariantsByGRanges html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient'
** testing if installed package can be loaded from final location
No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'GA4GHclient' ...
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient'
* MD5 sums
packaged installation of 'GA4GHclient' as GA4GHclient_1.16.0.zip
* DONE (GA4GHclient)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GA4GHclient' successfully unpacked and MD5 sums checked
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GA4GHclient.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> library(testthat)
> library(GA4GHclient)
Loading required package: S4Vectors
Loading required package: stats4
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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient'
>
> test_check("GA4GHclient")
== Skipped tests ===============================================================
* On Bioconductor (84)
[ FAIL 0 | WARN 0 | SKIP 84 | PASS 10 ]
>
> proc.time()
user system elapsed
11.89 1.00 12.89
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GA4GHclient.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> library(testthat)
> library(GA4GHclient)
Loading required package: S4Vectors
Loading required package: stats4
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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient'
>
> test_check("GA4GHclient")
== Skipped tests ===============================================================
* On Bioconductor (84)
[ FAIL 0 | WARN 0 | SKIP 84 | PASS 10 ]
>
> proc.time()
user system elapsed
12.20 0.57 12.78
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GA4GHclient.Rcheck/examples_i386/GA4GHclient-Ex.timings
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GA4GHclient.Rcheck/examples_x64/GA4GHclient-Ex.timings
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