CRAN Package Check Results for Maintainer Jake Hughey <jakejhughey at gmail.com>

CRAN Package Check Results for Maintainer ‘Jake Hughey <jakejhughey at gmail.com>’

Last updated on 2022-09-11 12:56:45 CEST.

Package	ERROR	OK
deltaccd		13
limorhyde		13
limorhyde2		13
phers		13
pmparser	1	12
rsurveycto		9
seeker	6	7
simphony		13
spectr		13
tipa		13

Package phers

Current CRAN status: OK: 13

Version: 1.0.10
Check: tests
Result: ERROR
     Running 'testthat.R' [12s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(pmparser)
     >
     > test_check('pmparser')
     [ FAIL 4 | WARN 8 | SKIP 4 | PASS 64 ]

     == Skipped tests ===============================================================
     * On CRAN (4)

     == Failed tests ================================================================
     -- 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 4 | WARN 8 | SKIP 4 | PASS 64 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Package rsurveycto

Current CRAN status: OK: 9

Package seeker

Current CRAN status: ERROR: 6, OK: 7

Version: 1.0.9
Check: tests
Result: ERROR
     Running 'testthat.R' [82s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(seeker)
     >
     > test_check('seeker')
     qs v0.25.4.
     trying URL 'https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-724/A-MEXP-724.adf.txt'
     Content type 'text/plain' length 5928030 bytes (5.7 MB)
     ==================================================
     downloaded 5.7 MB

     trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2755/E-MEXP-2755.sdrf.txt'
     Content type 'text/plain' length 4803 bytes
     ==================================================
     downloaded 4803 bytes

     trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2755/E-MEXP-2755.idf.txt'
     Content type 'text/plain' length 3832 bytes
     ==================================================
     downloaded 3832 bytes

     Copying raw data files

     trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2755/E-MEXP-2755.raw.1.zip'
     Content type 'application/zip' length 60875754 bytes (58.1 MB)
     ===============
     downloaded 18.5 MB

     Error in download.file(url, filedest, mode = "wb") :
     download from 'https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2755/E-MEXP-2755.raw.1.zip' failed
     [ FAIL 1 | WARN 3 | SKIP 22 | PASS 24 ]

     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (14)
     • On Windows (8)

     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-array-utils.R:104:3): getNaiveEsetAe unsupported ──────────────
     `filesObs` (`actual`) not equal to `filesExp` (`expected`).

     actual | expected
     [1] "A-MEXP-724.adf.txt" | "A-MEXP-724.adf.txt" [1]
     [2] "E-MEXP-2755.idf.txt" | "E-MEXP-2755.idf.txt" [2]
     [3] "E-MEXP-2755.raw.1.zip" -
     [4] "E-MEXP-2755.sdrf.txt" | "E-MEXP-2755.sdrf.txt" [3]

     [ FAIL 1 | WARN 3 | SKIP 22 | PASS 24 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64

Version: 1.0.9
Check: package dependencies
Result: ERROR
    Packages required but not available: 'ArrayExpress', 'tximport'

    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64

Version: 1.0.9
Check: package dependencies
Result: ERROR
    Package required but not available: ‘ArrayExpress’

    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.0.9
Check: tests
Result: ERROR
     Running 'testthat.R' [81s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(seeker)
     >
     > test_check('seeker')
     qs v0.25.4.
     trying URL 'https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-724/A-MEXP-724.adf.txt'
     Content type 'text/plain' length 5928030 bytes (5.7 MB)
     ==================================================
     downloaded 5.7 MB

     trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2755/E-MEXP-2755.sdrf.txt'
     Content type 'text/plain' length 4803 bytes
     ==================================================
     downloaded 4803 bytes

     trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2755/E-MEXP-2755.idf.txt'
     Content type 'text/plain' length 3832 bytes
     ==================================================
     downloaded 3832 bytes

     Copying raw data files

     trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2755/E-MEXP-2755.raw.1.zip'
     Content type 'application/zip' length 60875754 bytes (58.1 MB)
     ================
     downloaded 19.2 MB

     Error in download.file(url, filedest, mode = "wb") :
     download from 'https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2755/E-MEXP-2755.raw.1.zip' failed
     [ FAIL 1 | WARN 3 | SKIP 22 | PASS 24 ]

     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (14)
     • On Windows (8)

     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-array-utils.R:104:3): getNaiveEsetAe unsupported ──────────────
     `filesObs` (`actual`) not equal to `filesExp` (`expected`).

     actual | expected
     [1] "A-MEXP-724.adf.txt" | "A-MEXP-724.adf.txt" [1]
     [2] "E-MEXP-2755.idf.txt" | "E-MEXP-2755.idf.txt" [2]
     [3] "E-MEXP-2755.raw.1.zip" -
     [4] "E-MEXP-2755.sdrf.txt" | "E-MEXP-2755.sdrf.txt" [3]

     [ FAIL 1 | WARN 3 | SKIP 22 | PASS 24 ]
     Error: Test failures
     Execution halted
Flavor: r-release-windows-x86_64

Package simphony

Current CRAN status: OK: 13

Package spectr

Current CRAN status: OK: 13

Package tipa

Current CRAN status: OK: 13