| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:32 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the Gviz package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 867/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Gviz 1.43.0 (landing page) Robert Ivanek
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
| Package: Gviz |
| Version: 1.43.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Gviz.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Gviz_1.43.0.tar.gz |
| StartedAt: 2022-12-29 00:24:41 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 00:34:24 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 583.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Gviz.Rcheck |
| Warnings: NA |
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Gviz.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Gviz_1.43.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Gviz.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Gviz/DESCRIPTION' ... OK
* this is package 'Gviz' version '1.43.0'
* 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 'Gviz' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
R 1.7Mb
extdata 2.5Mb
* 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
* 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 ... WARNING
checkRd: (5) AlignmentsTrack-class.Rd:131-134: \item in \describe must have non-empty label
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checkRd: (5) settings.Rd:2071-2072: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2074-2075: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2077-2078: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2080-2081: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2083-2085: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2087-2088: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2090-2091: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2093-2095: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2097-2099: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2101-2103: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2105-2107: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2109-2111: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2113-2114: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2116-2117: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2119-2124: \item in \describe must have non-empty label
checkRd: (5) settings.Rd:2126-2127: \item in \describe must have non-empty label
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SequenceTrack-class 19.62 0.16 19.81
AlignmentsTrack-class 11.20 0.29 11.50
AnnotationTrack-class 6.18 0.02 6.19
GeneRegionTrack-class 5.03 0.09 5.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
7. └─Gviz:::.getBiomart(genome)
8. └─biomaRt::useEnsembl(biomart = "ensembl", dataset = map$dataset)
9. └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
10. └─biomaRt:::.getAttributes(mart, verbose = verbose)
11. └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
12. └─biomaRt:::bmRequest(...)
13. └─httr::GET(...)
14. └─httr:::request_perform(req, hu$handle$handle)
15. ├─httr:::request_fetch(req$output, req$url, handle)
16. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
17. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 293 ]
Error: Test failures
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: 1 ERROR, 1 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Gviz.Rcheck/00check.log'
for details.
Gviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Gviz ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'Gviz' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (Gviz)
Gviz.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64 (64-bit)
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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> library(testthat)
> library(Gviz)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
>
> test_check("Gviz")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 293 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_AllClasses.R:175'): interaction with biomart works ─────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.ensembl.org:443] Operation timed out after 10005 milliseconds with 99296 bytes received
Backtrace:
▆
1. └─Gviz::BiomartGeneRegionTrack(...) at test_AllClasses.R:175:4
2. └─Gviz:::.genome2Dataset(genome)
3. ├─Gviz::.doCache(...)
4. │ ├─BiocGenerics::eval(expression, envir = callEnv)
5. │ └─base::eval(expression, envir = callEnv)
6. │ └─base::eval(expression, envir = callEnv)
7. └─Gviz:::.getBiomart(genome)
8. └─biomaRt::useEnsembl(biomart = "ensembl", dataset = map$dataset)
9. └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
10. └─biomaRt:::.getAttributes(mart, verbose = verbose)
11. └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
12. └─biomaRt:::bmRequest(...)
13. └─httr::GET(...)
14. └─httr:::request_perform(req, hu$handle$handle)
15. ├─httr:::request_fetch(req$output, req$url, handle)
16. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
17. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 293 ]
Error: Test failures
Execution halted
Gviz.Rcheck/Gviz-Ex.timings
| name | user | system | elapsed | |
| AlignmentsTrack-class | 11.20 | 0.29 | 11.50 | |
| AnnotationTrack-class | 6.18 | 0.02 | 6.19 | |
| BiomartGeneRegionTrack-class | 3.17 | 0.03 | 3.21 | |
| CustomTrack-class | 0 | 0 | 0 | |
| DataTrack-class | 1.72 | 0.03 | 1.75 | |
| DisplayPars-class | 0.01 | 0.00 | 0.01 | |
| GdObject-class | 0.45 | 0.00 | 0.45 | |
| GeneRegionTrack-class | 5.03 | 0.09 | 5.14 | |
| GenomeAxisTrack-class | 3.10 | 0.05 | 3.14 | |
| HighlightTrack-class | 0.12 | 0.00 | 0.13 | |
| IdeogramTrack-class | 1.06 | 0.02 | 1.07 | |
| ImageMap-class | 0 | 0 | 0 | |
| OverlayTrack-class | 0.03 | 0.00 | 0.04 | |
| RangeTrack-class | 0.36 | 0.00 | 0.35 | |
| ReferenceTrack-class | 1.52 | 0.04 | 1.57 | |
| SequenceTrack-class | 19.62 | 0.16 | 19.81 | |
| StackedTrack-class | 0.72 | 0.05 | 0.77 | |
| UcscTrack | 0.82 | 0.01 | 0.84 | |
| exportTracks | 0.11 | 0.00 | 0.11 | |
| plotTracks | 3.95 | 0.02 | 4.01 | |
| settings | 0.73 | 0.00 | 0.74 | |