Last updated on 2022-04-24 03:52:56 CEST.
| Package | ERROR | OK |
|---|---|---|
| deltaccd | 12 | |
| limorhyde | 12 | |
| limorhyde2 | 12 | |
| pmparser | 3 | 9 |
| simphony | 12 | |
| spectr | 12 | |
| tipa | 12 |
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: ERROR: 3, OK: 9
Version: 1.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/292s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
remoteDir
download(glue("{remoteDir}{f$sub_dir}/{f[[col]]}"), file.path(localDir,
f$sub_dir, f[[col]]))
}`: task 2 failed - "cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed22n1116.xml.gz'"
Backtrace:
▆
1. └─pmparser:::getPubmedFiles(dFilePre, localDir, downloadMd5 = FALSE) at test_get_pubmed_files.R:30:2
2. └─... %dopar% ...
3. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
[ FAIL 1 | WARN 6 | SKIP 0 | PASS 185 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.0.4
Check: tests
Result: ERROR
Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(pmparser)
>
> test_check('pmparser')
Der Befehl "powershell" ist entweder falsch geschrieben oder
konnte nicht gefunden werden.
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed22n1113.xml.gz.md5'
Content length 60 bytes
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed22n1116.xml.gz.md5'
Content length 60 bytes
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed22n1113.xml.gz'
length 58838471 bytes (56.1 MB)
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed22n1116.xml.gz'
length 88307123 bytes (84.2 MB)
==================================================
[ FAIL 5 | WARN 11 | SKIP 0 | PASS 69 ]
== Failed tests ================================================================
-- Error (test_get_citation.R:21:3): getCitation -------------------------------
Error in `setnames(dCitation, dCols$old, dCols$new)`: Items of 'old' not found in column names: [citing, referenced]. Consider skip_absent=TRUE.
Backtrace:
x
1. \-pmparser::getCitation(...) at test_get_citation.R:21:2
2. \-data.table::setnames(dCitation, dCols$old, dCols$new)
-- Error (test_modify_pubmed_db_dup.R:51:3): modifyPubmedDb create is unique ---
Error in `gzfile(file, open = "rb")`: cannot open the connection
Backtrace:
x
1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:2
2. \-pmparser::getCitation(...)
3. \-pmparser:::writeTableInChunks(...)
4. +-R.utils::countLines(path)
5. \-R.utils::countLines.default(path)
6. \-base::gzfile(file, open = "rb")
-- Error (test_modify_pubmed_db_dup.R:67:3): modifyPubmedDb update is unique ---
Error in `gzfile(file, open = "rb")`: cannot open the connection
Backtrace:
x
1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:67:2
2. \-pmparser::getCitation(...)
3. \-pmparser:::writeTableInChunks(...)
4. +-R.utils::countLines(path)
5. \-R.utils::countLines.default(path)
6. \-base::gzfile(file, open = "rb")
-- Error (test_modify_pubmed_db_std.R:22:3): modifyPubmedDb create matches standard --
Error in `gzfile(file, open = "rb")`: cannot open the connection
Backtrace:
x
1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:2
2. \-pmparser::getCitation(...)
3. \-pmparser:::writeTableInChunks(...)
4. +-R.utils::countLines(path)
5. \-R.utils::countLines.default(path)
6. \-base::gzfile(file, open = "rb")
-- Error (test_modify_pubmed_db_std.R:42:3): modifyPubmedDb update matches standard --
Error in `gzfile(file, open = "rb")`: cannot open the connection
Backtrace:
x
1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:42:2
2. \-pmparser::getCitation(...)
3. \-pmparser:::writeTableInChunks(...)
4. +-R.utils::countLines(path)
5. \-R.utils::countLines.default(path)
6. \-base::gzfile(file, open = "rb")
[ FAIL 5 | WARN 11 | SKIP 0 | PASS 69 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: OK: 12