| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:39:29 -0400 (Wed, 16 Oct 2019).
| Package 1359/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| restfulSE 1.6.1 Shweta Gopaulakrishnan
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: restfulSE |
| Version: 1.6.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:restfulSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings restfulSE_1.6.1.tar.gz |
| StartedAt: 2019-10-16 06:27:29 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:45:00 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1050.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: restfulSE.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:restfulSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings restfulSE_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/restfulSE.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'restfulSE/DESCRIPTION' ... OK
* this is package 'restfulSE' version '1.6.1'
* package encoding: UTF-8
* 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 'restfulSE' 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 ... NOTE
BQ3_Source: no visible binding for global variable
'SampleTypeLetterCode'
BQ3m2: no visible binding for global variable 'SampleTypeLetterCode'
Undefined global functions or variables:
SampleTypeLetterCode
* 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' ... ERROR
Running examples in 'restfulSE-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RESTfulSummarizedExperiment
> ### Title: Construct RESTfulSummarizedExperiment
> ### Aliases: RESTfulSummarizedExperiment
> ### RESTfulSummarizedExperiment,RangedSummarizedExperiment,H5S_dataset-method
> ### .RESTfulSummarizedExperiment assay
> ### assay,RESTfulSummarizedExperiment,missing-method
>
> ### ** Examples
>
> require("rhdf5client")
Loading required package: rhdf5client
> hsds = H5S_source(serverURL=URL_hsds())
Error in transl(target) :
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
Calls: H5S_source -> hsdsInfo -> hsdsInfo -> transl
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'restfulSE-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RESTfulSummarizedExperiment
> ### Title: Construct RESTfulSummarizedExperiment
> ### Aliases: RESTfulSummarizedExperiment
> ### RESTfulSummarizedExperiment,RangedSummarizedExperiment,H5S_dataset-method
> ### .RESTfulSummarizedExperiment assay
> ### assay,RESTfulSummarizedExperiment,missing-method
>
> ### ** Examples
>
> require("rhdf5client")
Loading required package: rhdf5client
> hsds = H5S_source(serverURL=URL_hsds())
Error in transl(target) :
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
Calls: H5S_source -> hsdsInfo -> hsdsInfo -> transl
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))
== testthat results ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
1. Error: H5S_source completes (@test_reSE.R#9)
2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51)
3. Error: dim compatibility check is sensitive (@test_reSE.R#121)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))
== testthat results ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
1. Error: H5S_source completes (@test_reSE.R#9)
2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51)
3. Error: dim compatibility check is sensitive (@test_reSE.R#121)
Error: testthat unit tests failed
Execution halted
* 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: 4 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/restfulSE.Rcheck/00check.log'
for details.
restfulSE.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/restfulSE_1.6.1.tar.gz && rm -rf restfulSE.buildbin-libdir && mkdir restfulSE.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=restfulSE.buildbin-libdir restfulSE_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL restfulSE_1.6.1.zip && rm restfulSE_1.6.1.tar.gz restfulSE_1.6.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* installing *source* package 'restfulSE' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'restfulSE'
finding HTML links ... done
BQ3_Array-class html
BQ3_Array html
BQ3_ArraySeed-class html
BQ3_Matrix-class html
BQ3_Source-class html
BQ3_Source html
BQM_Array-class html
BQM_Array html
BQM_ArraySeed-class html
BQM_Matrix-class html
BQM_Source-class html
BQM_Source html
BQSummarizedExperiment html
RESTfulSummarizedExperiment-class html
RESTfulSummarizedExperiment html
assay-BQSummarizedExperiment-missing-method
html
assayNames-BQSummarizedExperiment-method
html
assays-RESTfulSummarizedExperiment-method
html
basic_clinvars html
bqConn html
cgcConn html
dim-BQ3_ArraySeed-method html
dim-BQM_ArraySeed-method html
dim-RESTfulSummarizedExperiment-method
html
dimnames-BQ3_ArraySeed-method html
dimnames-BQM_ArraySeed-method html
goPatt html
gtexTiss html
isbCgcDatasets html
isbCgcTables html
pancan_SE html
se100k html
seByTumor html
seByTumor_2016 html
tasicCortex html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* installing *source* package 'restfulSE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'restfulSE' as restfulSE_1.6.1.zip
* DONE (restfulSE)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'restfulSE' successfully unpacked and MD5 sums checked
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restfulSE.Rcheck/tests_i386/testthat.Rout.fail
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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, which.max, which.min
Loading required package: S4Vectors
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: 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, rowsum
> library(rhdf5client)
>
> test_check("restfulSE")
-- 1. Error: H5S_source completes (@test_reSE.R#9) ----------------------------
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:9
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))
-- 2. Error: RESTfulSummarizedExperiment infrastructure works against server (@t
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:51
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))
-- 3. Error: dim compatibility check is sensitive (@test_reSE.R#121) ----------
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))
== testthat results ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
1. Error: H5S_source completes (@test_reSE.R#9)
2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51)
3. Error: dim compatibility check is sensitive (@test_reSE.R#121)
Error: testthat unit tests failed
Execution halted
|
restfulSE.Rcheck/tests_x64/testthat.Rout.fail
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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, which.max, which.min
Loading required package: S4Vectors
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: 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, rowsum
> library(rhdf5client)
>
> test_check("restfulSE")
-- 1. Error: H5S_source completes (@test_reSE.R#9) ----------------------------
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:9
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))
-- 2. Error: RESTfulSummarizedExperiment infrastructure works against server (@t
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:51
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))
-- 3. Error: dim compatibility check is sensitive (@test_reSE.R#121) ----------
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))
== testthat results ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
1. Error: H5S_source completes (@test_reSE.R#9)
2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51)
3. Error: dim compatibility check is sensitive (@test_reSE.R#121)
Error: testthat unit tests failed
Execution halted
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restfulSE.Rcheck/examples_i386/restfulSE-Ex.timings
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restfulSE.Rcheck/examples_x64/restfulSE-Ex.timings
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