Sean Davis
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GenomicDataCommons |
| Branch: RELEASE_3_8 |
| Last Commit: 7bdc2aa |
| Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:27:43 -0400 (Sat, 13 Apr 2019).
| Package 624/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicDataCommons 1.6.0 Sean Davis
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: GenomicDataCommons |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicDataCommons.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GenomicDataCommons_1.6.0.tar.gz |
| StartedAt: 2019-04-13 02:32:53 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:37:47 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 293.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicDataCommons.Rcheck |
| Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicDataCommons.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GenomicDataCommons_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicDataCommons.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GenomicDataCommons/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GenomicDataCommons' version '1.6.0' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 'GenomicDataCommons' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAlTc6F/R.INSTALL14285cdd5a3a/GenomicDataCommons/man/gdc_rnaseq.Rd:28: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAlTc6F/R.INSTALL14285cdd5a3a/GenomicDataCommons/man/readDNAcopy.Rd:12: file link 'read_tsv' in package 'readr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAlTc6F/R.INSTALL14285cdd5a3a/GenomicDataCommons/man/readDNAcopy.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAlTc6F/R.INSTALL14285cdd5a3a/GenomicDataCommons/man/readHTSeqFile.Rd:16: file link 'read_tsv' in package 'readr' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicDataCommons.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 ... NOTE default_fields.character: no visible binding for global variable 'defaults' gdc_rnaseq: no visible binding for global variable 'case_id' gdc_rnaseq: no visible binding for global variable 'file_id' Undefined global functions or variables: case_id defaults file_id * 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 ... WARNING Undocumented arguments in documentation object '.htseq_importer' 'fnames' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... 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: 2 WARNINGs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicDataCommons.Rcheck/00check.log' for details.
GenomicDataCommons.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GenomicDataCommons_1.6.0.tar.gz && rm -rf GenomicDataCommons.buildbin-libdir && mkdir GenomicDataCommons.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GenomicDataCommons_1.6.0.zip && rm GenomicDataCommons_1.6.0.tar.gz GenomicDataCommons_1.6.0.zip
###
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install for i386
* installing *source* package 'GenomicDataCommons' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicDataCommons'
finding HTML links ... done
GenomicDataCommons html
aggregations html
available_expand html
available_fields html
available_values html
constants html
count html
default_fields html
dot-htseq_importer html
entity_name html
expand html
faceting html
filtering html
gdc_cache html
gdc_client html
gdc_clinical html
gdc_rnaseq html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAlTc6F/R.INSTALL14285cdd5a3a/GenomicDataCommons/man/gdc_rnaseq.Rd:28: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
gdc_token html
gdcdata html
grep_fields html
id_field html
ids html
make_filter html
manifest html
mapping html
query html
readDNAcopy html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAlTc6F/R.INSTALL14285cdd5a3a/GenomicDataCommons/man/readDNAcopy.Rd:12: file link 'read_tsv' in package 'readr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAlTc6F/R.INSTALL14285cdd5a3a/GenomicDataCommons/man/readDNAcopy.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
readHTSeqFile html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAlTc6F/R.INSTALL14285cdd5a3a/GenomicDataCommons/man/readHTSeqFile.Rd:16: file link 'read_tsv' in package 'readr' does not exist and so has been treated as a topic
response html
results html
results_all html
select html
slicing html
status html
transfer html
write_manifest html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GenomicDataCommons' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicDataCommons' as GenomicDataCommons_1.6.0.zip
* DONE (GenomicDataCommons)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GenomicDataCommons' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GenomicDataCommons.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(GenomicDataCommons)
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Attaching package: 'GenomicDataCommons'
The following object is masked from 'package:stats':
filter
>
> test_check("GenomicDataCommons")
== testthat results ===========================================================
OK: 48 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
9.46 0.89 19.36
|
GenomicDataCommons.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(GenomicDataCommons)
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Attaching package: 'GenomicDataCommons'
The following object is masked from 'package:stats':
filter
>
> test_check("GenomicDataCommons")
== testthat results ===========================================================
OK: 48 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
8.46 0.34 27.87
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GenomicDataCommons.Rcheck/examples_i386/GenomicDataCommons-Ex.timings
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GenomicDataCommons.Rcheck/examples_x64/GenomicDataCommons-Ex.timings
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