| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 198/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbKegg 1.6.1 (landing page) Pierrick Roger
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the biodbKegg package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbKegg |
| Version: 1.6.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.6.1.tar.gz |
| StartedAt: 2023-10-17 05:44:10 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 06:08:17 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 1446.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbKegg.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.6.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biodbKegg.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbKegg/DESCRIPTION’ ... OK
* this is package ‘biodbKegg’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biodbKegg’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
KeggEnzymeConn 11.947 0.525 128.933
KeggCompoundConn 3.462 0.687 16.769
KeggPathwayConn 2.689 0.176 47.147
* 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:
3. └─biodb (local) initialize(...)
4. └─private$loadBiodbPkgsDefinitions(c(biodb = packageVersion("biodb")))
5. └─self$loadDefinitions(file, package = pkg)
6. └─self$getConfig()$define(def$config)
7. ├─base::do.call(private$newKey, v)
8. └─biodb (local) `<fn>`(...)
9. └─private$getSvnBinaryPath()
10. └─base::Sys.which("svn")
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. └─base::system(...)
[ FAIL 46 | WARN 0 | SKIP 0 | PASS 1007 ]
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
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biodbKegg.Rcheck/00check.log’
for details.
biodbKegg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbKegg ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘biodbKegg’ ... ** using staged installation ** R ** 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 (biodbKegg)
biodbKegg.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbKegg)
> Sys.setenv(TESTTHAT_REPORTER = "summary")
> test_check("biodbKegg")
[ FAIL 46 | WARN 0 | SKIP 0 | PASS 1007 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_100_compound.R:151:5'): addInfo() works correctly. ─────────────
Error in `FUN(X[[i]], ...)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbKegg (local) `<fn>`(conn = `<KggCmpnC>`)
3. └─conn$addInfo(x, id.col = "ids", org = "mmu") at test_100_compound.R:151:4
4. └─self$getBiodb()$entriesFieldToVctOrLst(...)
5. └─base::lapply(...)
6. └─biodb (local) FUN(X[[i]], ...)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(`1.1.1.165` = "1.1.1.165") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(`1.1.1.165` = "1.1.1.165") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by name. ──────────────────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 1.1.1.165 by name "2-alkyn-1-ol dehydrogenase".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for an entry by name. ──────────────────────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 1.1.1.165 by name "2-alkyn-1-ol dehydrogenase".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
── Failure ('test_200_enzyme.R:34:5'): issue 340 is corrected. ─────────────────
all(right_pws %in% pws) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbKegg (local) `<fn>`(conn = `<KggEnzyC>`)
3. └─testthat::expect_true(all(right_pws %in% pws)) at test_200_enzyme.R:34:4
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(`mmu%3A14635` = "mmu:14635") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(`mmu%3A14635` = "mmu:14635") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by name. ──────────────────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry mmu:14635 by name "(RefSeq) galactokinase 1".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for an entry by name. ──────────────────────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry mmu:14635 by name "(RefSeq) galactokinase 1".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(G00018 = "G00018") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(G00018 = "G00018") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by name. ──────────────────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry G00018 by name "DS 3".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for an entry by name. ──────────────────────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry G00018 by name "DS 3".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(M00009 = "M00009") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(M00009 = "M00009") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by name. ──────────────────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry M00009 by name "Citrate cycle (TCA cycle, Krebs cycle)".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for an entry by name. ──────────────────────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry M00009 by name "Citrate cycle (TCA cycle, Krebs cycle)".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
── Error ('test_500_orthology.R:11:1'): (code run outside of `test_that()`) ────
<cmdError/error/condition>
Error in `system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)`: cannot popen '/usr/bin/which 'svn' 2>/dev/null', probable reason 'Too many open files'
Backtrace:
▆
1. └─biodb::createBiodbTestInstance(ack = TRUE) at test_500_orthology.R:11:0
2. └─BiodbMain$new(autoloadExtraPkgs = FALSE)
3. └─biodb (local) initialize(...)
4. └─private$loadBiodbPkgsDefinitions(c(biodb = packageVersion("biodb")))
5. └─self$loadDefinitions(file, package = pkg)
6. └─self$getConfig()$define(def$config)
7. ├─base::do.call(private$newKey, v)
8. └─biodb (local) `<fn>`(...)
9. └─private$getSvnBinaryPath()
10. └─base::Sys.which("svn")
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. └─base::system(...)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(map00053 = "map00053") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by searchable field ───────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(map00053 = "map00053") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): We can search for an entry by name. ──────────────────────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry map00053 by name "Ascorbate and aldarate metabolism".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for an entry by name. ──────────────────────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry map00053 by name "Ascorbate and aldarate metabolism".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure (???): The entry page URL can be downloaded. ────────────────────────
!is.na(content) is not TRUE
`actual`:
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
3. └─testthat::expect_true(!is.na(content))
── Failure (???): The entry page URL can be downloaded. ────────────────────────
nchar(content) > 0 is not TRUE
`actual`:
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
3. └─testthat::expect_true(nchar(content) > 0)
── Error ('test_600_pathway.R:28:5'): We can build a decorated pathway graph. ──
Error in `biodb::error0("Impossible to find pathway image path inside",
" HTML page for pathway ID ", id, ".")`: Impossible to find pathway image path inside HTML page for pathway ID mmu00260.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbKegg (local) `<fn>`(conn = `<KggPthwC>`)
3. └─conn$getDecoratedGraphPicture("mmu00260", color2ids = c) at test_600_pathway.R:28:4
4. └─private$getPathwayImage(id)
5. └─biodb::error0(...)
── Error ('test_600_pathway.R:45:5'): getDecoratedGraphPicture() does not fail when called with
unexisting compounds. ──
Error in `biodb::error0("Impossible to find pathway image path inside",
" HTML page for pathway ID ", id, ".")`: Impossible to find pathway image path inside HTML page for pathway ID mmu00260.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbKegg (local) `<fn>`(conn = `<KggPthwC>`)
3. └─conn$getDecoratedGraphPicture("mmu00260", color2ids = c) at test_600_pathway.R:45:4
4. └─private$getPathwayImage(id)
5. └─biodb::error0(...)
── Failure ('test_600_pathway.R:68:9'): extractPathwayMapShapes() works correctly. ──
`shapes` has length 0, not length 2.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbKegg (local) `<fn>`(conn = `<KggPthwC>`)
3. └─testthat::expect_length(shapes, items[[i]]) at test_600_pathway.R:68:8
── Failure ('test_600_pathway.R:68:9'): extractPathwayMapShapes() works correctly. ──
`shapes` has length 0, not length 2.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbKegg (local) `<fn>`(conn = `<KggPthwC>`)
3. └─testthat::expect_length(shapes, items[[i]]) at test_600_pathway.R:68:8
── Failure ('test_600_pathway.R:68:9'): extractPathwayMapShapes() works correctly. ──
`shapes` has length 0, not length 2.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbKegg (local) `<fn>`(conn = `<KggPthwC>`)
3. └─testthat::expect_length(shapes, items[[i]]) at test_600_pathway.R:68:8
── Failure ('test_600_pathway.R:68:9'): extractPathwayMapShapes() works correctly. ──
`shapes` has length 0, not length 1.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbKegg (local) `<fn>`(conn = `<KggPthwC>`)
3. └─testthat::expect_length(shapes, items[[i]]) at test_600_pathway.R:68:8
── Error ('test_700_reaction.R:5:1'): (code run outside of `test_that()`) ──────
<cmdError/error/condition>
Error in `system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)`: cannot popen '/usr/bin/which 'svn' 2>/dev/null', probable reason 'Too many open files'
Backtrace:
▆
1. └─biodb::createBiodbTestInstance(ack = TRUE) at test_700_reaction.R:5:0
2. └─BiodbMain$new(autoloadExtraPkgs = FALSE)
3. └─biodb (local) initialize(...)
4. └─private$loadBiodbPkgsDefinitions(c(biodb = packageVersion("biodb")))
5. └─self$loadDefinitions(file, package = pkg)
6. └─self$getConfig()$define(def$config)
7. ├─base::do.call(private$newKey, v)
8. └─biodb (local) `<fn>`(...)
9. └─private$getSvnBinaryPath()
10. └─base::Sys.which("svn")
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. └─base::system(...)
[ FAIL 46 | WARN 0 | SKIP 0 | PASS 1007 ]
Error: Test failures
Execution halted
biodbKegg.Rcheck/biodbKegg-Ex.timings
| name | user | system | elapsed | |
| KeggCircle | 0.055 | 0.001 | 0.065 | |
| KeggCompoundConn | 3.462 | 0.687 | 16.769 | |
| KeggCompoundEntry | 0.499 | 0.024 | 2.409 | |
| KeggConn | 0.406 | 0.020 | 3.509 | |
| KeggEntry | 0.435 | 0.018 | 0.630 | |
| KeggEnzymeConn | 11.947 | 0.525 | 128.933 | |
| KeggEnzymeEntry | 0.519 | 0.022 | 2.320 | |
| KeggGenesConn | 0.576 | 0.025 | 2.527 | |
| KeggGenesEntry | 0.512 | 0.017 | 0.758 | |
| KeggGlycanConn | 0.415 | 0.015 | 0.674 | |
| KeggGlycanEntry | 0.565 | 0.024 | 2.501 | |
| KeggModuleConn | 0.699 | 0.028 | 2.521 | |
| KeggModuleEntry | 0.409 | 0.017 | 0.551 | |
| KeggOrthologyConn | 0.555 | 0.022 | 2.796 | |
| KeggOrthologyEntry | 0.517 | 0.017 | 0.773 | |
| KeggPathwayConn | 2.689 | 0.176 | 47.147 | |
| KeggPathwayEntry | 0.464 | 0.021 | 2.090 | |
| KeggReactionConn | 0.459 | 0.022 | 2.192 | |
| KeggReactionEntry | 0.417 | 0.015 | 0.542 | |
| KeggRect | 0.003 | 0.000 | 0.005 | |
| KeggShape | 0.001 | 0.000 | 0.002 | |