CRAN Package Check Results for Maintainer ‘Carl Boettiger <cboettig at gmail.com>’

Last updated on 2020-12-02 00:48:29 CET.

Package FAIL ERROR WARN NOTE OK
arkdb 12
codemetar 1 4 7
contentid 1 11
EcoNetGen 12
EML 12
emld 1 11
neonstore 12
piggyback 12
pmc 1 11
rdflib 3 9
rfigshare 12
rfishbase 1 5 6
RNeXML 7 5
sarsop 7 5
taxadb 11 1
treebase 12
virtuoso 1 11

Package arkdb

Current CRAN status: OK: 12

Package codemetar

Current CRAN status: ERROR: 1, NOTE: 4, OK: 7

Version: 0.1.9
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘memoise’ ‘pkgbuild’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.1.9
Check: package dependencies
Result: ERROR
    Package required but not available: ‘gert’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-patched-solaris-x86

Package contentid

Current CRAN status: ERROR: 1, OK: 11

Version: 0.0.8
Check: examples
Result: ERROR
    Running examples in ‘contentid-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: resolve
    > ### Title: Resolve content from a content identifier
    > ### Aliases: resolve
    >
    > ### ** Examples
    >
    > ## Don't show:
    > ## Real users won't use a temporary dir
    > Sys.setenv("CONTENTID_REGISTRIES" = tempdir())
    > ## End(Don't show)
    > # ensure some content in local storage for testing purposes:
    > vostok_co2 <- system.file("extdata", "vostok.icecore.co2",
    + package = "contentid")
    > store(vostok_co2)
    Error: [EROFS] Failed to make directory '/Users/urbanek/Library/Application Support/contentid': read-only file system
    Execution halted
Flavor: r-oldrel-macos-x86_64

Package EcoNetGen

Current CRAN status: OK: 12

Package EML

Current CRAN status: OK: 12

Package emld

Current CRAN status: NOTE: 1, OK: 11

Version: 0.5.1
Check: installed package size
Result: NOTE
     installed size is 5.3Mb
     sub-directories of 1Mb or more:
     xsd 4.1Mb
Flavor: r-patched-solaris-x86

Package neonstore

Current CRAN status: OK: 12

Package piggyback

Current CRAN status: OK: 12

Package pmc

Current CRAN status: FAIL: 1, OK: 11

Version: 1.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘pmc_tutorial.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Loading required package: ape
    Loading required package: subplex
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    Attaching package: 'gridExtra'
    
    The following object is masked from 'package:dplyr':
    
     combine
    
    Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
     Parameter estimates appear at bounds:
     lambda
    Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
     Parameter estimates appear at bounds:
     lambda
    Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
     Parameter estimates appear at bounds:
     lambda
    Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
     Parameter estimates appear at bounds:
     lambda
    
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 1.0.3
Check: PDF version of manual
Result: FAIL
Flavor: r-oldrel-macos-x86_64

Package rdflib

Current CRAN status: WARN: 3, OK: 9

Version: 0.2.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘rdf_intro.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Quitting from lines 41-42 (rdf_intro.Rmd)
    Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
    there is no package called 'webshot'
    --- failed re-building ‘rdf_intro.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘rdf_intro.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘rdf_intro.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Quitting from lines 41-42 (rdf_intro.Rmd)
    Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘rdf_intro.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘rdf_intro.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Package rfigshare

Current CRAN status: NOTE: 12

Version: 0.3.7
Check: R code for possible problems
Result: NOTE
    fs_author_ids : <anonymous>: no visible global function definition for
     'select.list'
    fs_download : <anonymous>: no visible global function definition for
     'download.file'
    Undefined global functions or variables:
     download.file select.list
    Consider adding
     importFrom("utils", "download.file", "select.list")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Package rfishbase

Current CRAN status: ERROR: 1, NOTE: 5, OK: 6

Version: 3.0.4
Check: data for non-ASCII characters
Result: NOTE
     Note: found 44 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 3.0.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [3s/125s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(rfishbase)
     > options(is_test = TRUE) # set user-agent to distinguish automated tests
     >
     >
     > Sys.setenv(GITHUB_TOKEN=paste0("b2b7441d", "aeeb010b", "1df26f1f6", "0a7f1ed",
     + "c485e443"))
     >
     > test_check("rfishbase")
     ── Skip (test_commonnames.R:5:3): test common to sci name ──────────────────────
     Reason: On CRAN
    
     ── Skip (test_commonnames.R:24:3): test sci to common names ────────────────────
     Reason: On CRAN
    
     ── Skip (test_distribution.R:4:3): We can query locations ──────────────────────
     Reason: On CRAN
    
     ── Skip (test_ecology.R:3:3): we can call the ecology table ────────────────────
     Reason: On CRAN
    
     ── Skip (test_ecology.R:13:3): We can query trophic level fields only ──────────
     Reason: On CRAN
    
     ── Skip (test_endpoint.R:9:3): Custom queries give desired result ──────────────
     Reason: On CRAN
    
     ── Skip (test_list_fields.R:5:3): we can search for a field name ───────────────
     Reason: On CRAN
    
     ── Skip (test_load_taxa.R:5:3): We can load taxa from online ───────────────────
     Reason: On CRAN
    
     ── Skip (test_maturity.R:5:13): returns a data.frame with correct sciname ──────
     Reason: On CRAN
    
     ── Skip (test_morpho_physio.R:5:3): population_dynamics methods can all be calle
     Reason: On CRAN
    
     ── Skip (test_population_dynamics.R:5:3): population_dynamics methods can all be
     Reason: On CRAN
    
     ── Skip (test_species.R:4:3): We can extract generic information from the specie
     Reason: On CRAN
    
     ── Skip (test_species.R:12:3): Check some classes and values of species table ──
     Reason: On CRAN
    
     ── Skip (test_species.R:21:3): We can pass a species_list based on taxanomic gro
     Reason: On CRAN
    
     ── Skip (test_species.R:32:3): We can pass a species_list based on taxanomic gro
     Reason: On CRAN
    
     ── Skip (test_species.R:43:3): We can filter on certain fields ─────────────────
     Reason: On CRAN
    
     ── Warning (test_species_list.R:5:3): We can pass a species_list based on taxano
     downloaded length 0 != reported length 2788345
    
     ── Warning (test_species_list.R:5:3): We can pass a species_list based on taxano
     URL 'https://github-production-release-asset-2e65be.s3.amazonaws.com/2799822/59f10180-968e-11e9-8fca-39b072e6c43d?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20201201%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20201201T025330Z&X-Amz-Expires=300&X-Amz-Signature=4724933712c71e9be33bd7e562be984e0632ffbf1fcf8653fd0d10977482e2b5&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=2799822&response-content-disposition=attachment%3B%20filename%3Dfb.2fspecies.tsv.bz2&response-content-type=application%2Foctet-stream': Timeout of 60 seconds was reached
    
     ── ERROR (test_species_list.R:5:3): We can pass a species_list based on taxanomi
     Error: download from 'https://github.com/ropensci/rfishbase/releases/download/fb-19.04/fb.2fspecies.tsv.bz2' failed
     Backtrace:
     █
     1. └─rfishbase::species_list(Genus = "Labroides") test_species_list.R:5:2
     2. └─rfishbase::load_taxa(server)
     3. ├─base::withVisible(`_f`(server = server, ... = ...))
     4. └─rfishbase:::`_f`(server = server, ... = ...)
     5. └─rfishbase:::fb_taxa_table(server)
     6. └─rfishbase:::fb_tbl("species", server)
     7. ├─base::withVisible(`_f`(tbl = tbl, server = server, ... = ...))
     8. └─rfishbase:::`_f`(tbl = tbl, server = server, ... = ...)
     9. └─utils::download.file(addr, tmp, quiet = TRUE)
    
     ── Warning (test_species_list.R:13:3): Look up species by SpecCode ─────────────
     URL 'https://github-production-release-asset-2e65be.s3.amazonaws.com/2799822/59f10180-968e-11e9-8fca-39b072e6c43d?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20201201%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20201201T025330Z&X-Amz-Expires=300&X-Amz-Signature=4724933712c71e9be33bd7e562be984e0632ffbf1fcf8653fd0d10977482e2b5&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=2799822&response-content-disposition=attachment%3B%20filename%3Dfb.2fspecies.tsv.bz2&response-content-type=application%2Foctet-stream': Timeout of 60 seconds was reached
    
     ── ERROR (test_species_list.R:13:3): Look up species by SpecCode ───────────────
     Error: cannot open URL 'https://github.com/ropensci/rfishbase/releases/download/fb-19.04/fb.2fspecies.tsv.bz2'
     Backtrace:
     █
     1. └─rfishbase::species_list(SpecCode = 5537) test_species_list.R:13:2
     2. └─rfishbase::load_taxa(server)
     3. ├─base::withVisible(`_f`(server = server, ... = ...))
     4. └─rfishbase:::`_f`(server = server, ... = ...)
     5. └─rfishbase:::fb_taxa_table(server)
     6. └─rfishbase:::fb_tbl("species", server)
     7. ├─base::withVisible(`_f`(tbl = tbl, server = server, ... = ...))
     8. └─rfishbase:::`_f`(tbl = tbl, server = server, ... = ...)
     9. └─utils::download.file(addr, tmp, quiet = TRUE)
    
     ── Skip (test_synonyms.R:6:3): synonyms can query by species ───────────────────
     Reason: On CRAN
    
     ── Skip (test_synonyms.R:15:3): synonyms can resolve misspellings ──────────────
     Reason: On CRAN
    
     ── Skip (test_synonyms.R:25:3): We can validate names ──────────────────────────
     Reason: On CRAN
    
     ── Skip (test_trophic_ecology.R:3:3): we can call the trpohic ecology informatio
     Reason: On CRAN
    
     ── Skipped tests ──────────────────────────────────────────────────────────────
     ● On CRAN (20)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     Warning (test_species_list.R:5:3): We can pass a species_list based on taxanomic group
     Warning (test_species_list.R:5:3): We can pass a species_list based on taxanomic group
     ERROR (test_species_list.R:5:3): We can pass a species_list based on taxanomic group
     Warning (test_species_list.R:13:3): Look up species by SpecCode
     ERROR (test_species_list.R:13:3): Look up species by SpecCode
    
     [ FAIL 2 | WARN 3 | SKIP 20 | PASS 5 ]
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64

Package RNeXML

Current CRAN status: NOTE: 7, OK: 5

Version: 2.4.5
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'knitcitations'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Package sarsop

Current CRAN status: NOTE: 7, OK: 5

Version: 0.6.5
Check: installed package size
Result: NOTE
     installed size is 52.9Mb
     sub-directories of 1Mb or more:
     bin 52.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Package taxadb

Current CRAN status: NOTE: 11, OK: 1

Additional issues

donttest

Version: 0.1.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'MonetDBLite'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 0.1.0
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘RSQLite’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.1.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'MonetDBLite', 'duckdb'
Flavor: r-release-macos-x86_64

Version: 0.1.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘duckdb’
Flavor: r-oldrel-macos-x86_64

Package treebase

Current CRAN status: OK: 12

Package virtuoso

Current CRAN status: ERROR: 1, OK: 11

Version: 0.1.5
Check: tests
Result: ERROR
     Running ‘spelling.R’ [0s/0s]
     Running ‘testthat.R’ [3s/3s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
    
     virtuoso isn't running.
     No active virtuoso process detected.
     ── Skipped tests ──────────────────────────────────────────────────────────────
     ● On CRAN (7)
     ● On Mac (1)
     ● has_virtuoso() is not TRUE (1)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     Warning (test-vos_odbc.R:25:3): We can generate an odbcinst file
     ERROR (test-vos_odbc.R:25:3): We can generate an odbcinst file
    
     [ FAIL 1 | WARN 1 | SKIP 9 | PASS 14 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-macos-x86_64