Last updated on 2025-01-18 07:51:08 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| deltaccd | 13 | ||
| limorhyde | 3 | 10 | |
| limorhyde2 | 13 | ||
| phers | 13 | ||
| pmparser | 1 | 12 | |
| seeker | 3 | 10 | |
| simphony | 13 | ||
| spectr | 13 | ||
| tipa | 13 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 3, OK: 10
Version: 1.0.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-arm64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-30 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 1.0.21
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/68s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pmparser)
>
> test_check('pmparser')
[ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3',
'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_modify_pubmed_db_dup.R:51:3'): modifyPubmedDb create is unique ──
<COULDNT_RESOLVE_HOST/GenericCurlError/error/condition>
Error in `function (type, msg, asError = TRUE)
{
if (!is.character(type)) {
i = match(type, CURLcodeValues)
typeName = if (is.na(i))
character()
else names(CURLcodeValues)[i]
}
typeName = gsub("^CURLE_", "", typeName)
fun = (if (asError)
stop
else warning)
fun(structure(list(message = msg, call = sys.call()), class = c(typeName,
"GenericCurlError", "error", "condition")))
}(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov", TRUE)`: Could not resolve host: ftp.ncbi.nlm.nih.gov
Backtrace:
▆
1. ├─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:3
2. │ └─pmparser:::getReadme(con = con)
3. │ └─RCurl::getURL(glue("{remoteDir}/{filename}"))
4. │ └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
5. └─RCurl (local) `<fn>`(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov", TRUE)
── Error ('test_modify_pubmed_db_dup.R:67:3'): modifyPubmedDb update is unique ──
Error in `{
dNow = getRemoteFilenames(glue("{remoteDir}/{subDir}/"),
pattern)
dNow[, `:=`(sub_dir, subDir)]
}`: task 1 failed - "Could not resolve host: ftp.ncbi.nlm.nih.gov"
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:67:3
2. └─pmparser:::getPubmedFileInfo(localDir, subDirs = subDir, con = conTmp)
3. └─foreach(subDir = subDirs, .combine = rbind) %do% ...
4. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
── Error ('test_modify_pubmed_db_std.R:22:3'): modifyPubmedDb create matches standard ──
<COULDNT_RESOLVE_HOST/GenericCurlError/error/condition>
Error in `function (type, msg, asError = TRUE)
{
if (!is.character(type)) {
i = match(type, CURLcodeValues)
typeName = if (is.na(i))
character()
else names(CURLcodeValues)[i]
}
typeName = gsub("^CURLE_", "", typeName)
fun = (if (asError)
stop
else warning)
fun(structure(list(message = msg, call = sys.call()), class = c(typeName,
"GenericCurlError", "error", "condition")))
}(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov", TRUE)`: Could not resolve host: ftp.ncbi.nlm.nih.gov
Backtrace:
▆
1. ├─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:3
2. │ └─pmparser:::getReadme(con = con)
3. │ └─RCurl::getURL(glue("{remoteDir}/{filename}"))
4. │ └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
5. └─RCurl (local) `<fn>`(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov", TRUE)
── Error ('test_modify_pubmed_db_std.R:42:3'): modifyPubmedDb update matches standard ──
Error in `{
dNow = getRemoteFilenames(glue("{remoteDir}/{subDir}/"),
pattern)
dNow[, `:=`(sub_dir, subDir)]
}`: task 1 failed - "Could not resolve host: ftp.ncbi.nlm.nih.gov"
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:42:3
2. └─pmparser:::getPubmedFileInfo(localDir, subDirs = subDir, con = conTmp)
3. └─foreach(subDir = subDirs, .combine = rbind) %do% ...
4. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
[ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-release-linux-x86_64
Current CRAN status: NOTE: 3, OK: 10
Version: 1.1.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavor: r-release-macos-arm64
Version: 1.1.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ArrayExpress’
Flavor: r-oldrel-macos-arm64
Version: 1.1.6
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘ArrayExpress’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.1.6
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'ArrayExpress', 'org.Mm.eg.db'
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13