CRAN Package Check Results for Package protti

Last updated on 2021-12-06 18:52:39 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.0 15.71 234.47 250.18 ERROR
r-devel-linux-x86_64-debian-gcc 0.2.0 14.18 170.86 185.04 ERROR
r-devel-linux-x86_64-fedora-clang 0.2.0 298.97 NOTE
r-devel-linux-x86_64-fedora-gcc 0.2.0 281.64 ERROR
r-devel-windows-x86_64-new-UL 0.2.0 40.00 295.00 335.00 OK
r-devel-windows-x86_64-new-TK 0.2.0 ERROR
r-devel-windows-x86_64-old 0.2.0 29.00 210.00 239.00 OK
r-patched-linux-x86_64 0.2.0 16.84 217.85 234.69 OK
r-release-linux-x86_64 0.2.0 13.09 222.89 235.98 OK
r-release-macos-arm64 0.2.0 NOTE
r-release-macos-x86_64 0.2.0 NOTE
r-release-windows-ix86+x86_64 0.2.0 36.00 271.00 307.00 OK
r-oldrel-macos-x86_64 0.2.0 NOTE
r-oldrel-windows-ix86+x86_64 0.2.0 34.00 284.00 318.00 OK

Check Details

Version: 0.2.0
Check: examples
Result: ERROR
    Running examples in 'protti-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: qc_sample_correlation
    > ### Title: Correlation based hirachical clustering of samples
    > ### Aliases: qc_sample_correlation
    >
    > ### ** Examples
    >
    > set.seed(123) # Makes example reproducible
    >
    > # Create example data
    > data <- create_synthetic_data(
    + n_proteins = 100,
    + frac_change = 0.05,
    + n_replicates = 3,
    + n_conditions = 2,
    + method = "effect_random"
    + )
    >
    > # Create sample correlation heatmap
    > qc_sample_correlation(
    + data = data,
    + sample = sample,
    + grouping = peptide,
    + intensity_log2 = peptide_intensity_missing,
    + condition = condition
    + )
    Error in ser_permutation_vector(order, method = method$name) :
     'list' object cannot be coerced to type 'integer'
    Calls: qc_sample_correlation ... seriate.dist -> ser_permutation -> ser_permutation_vector
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: tests
Result: ERROR
     Running 'testthat.R' [80s/92s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(protti)
     <U+0001F469><U+0001F3FD><U+200D><U+0001F52C> Welcome to protti version 0.2.0! <U+0001F468><U+0001F3FC><U+200D><U+0001F4BB>
    
     <U+0001F52C> Have fun analysing your data! <U+0001F4BB>
     >
     > test_check("protti")
     $`1`
    
     == Failed tests ================================================================
     -- Error (test-qc_functions.R:119:3): qc_sample_correlation works --------------
     Error in `ser_permutation_vector(order, method = method$name)`: 'list' object cannot be coerced to type 'integer'
     Backtrace:
     x
     1. \-protti::qc_sample_correlation(...) test-qc_functions.R:119:2
     2. \-dendextend::seriate_dendrogram(dendrogram, distance, method = "OLO")
     3. +-seriation::seriate(...)
     4. \-seriation:::seriate.dist(...)
     5. +-seriation::ser_permutation(ser_permutation_vector(order, method = method$name))
     6. \-seriation::ser_permutation_vector(order, method = method$name)
    
     [ FAIL 1 | WARN 0 | SKIP 0 | PASS 120 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.0
Check: tests
Result: ERROR
     Running β€˜testthat.R’ [55s/95s]
    Running the tests in β€˜tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(protti)
     πŸ‘©πŸ½β€πŸ”¬ Welcome to protti version 0.2.0! πŸ‘¨πŸΌβ€πŸ’»
    
     πŸ”¬ Have fun analysing your data! πŸ’»
     >
     > test_check("protti")
     $`1`
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test-qc_functions.R:119:3): qc_sample_correlation works ──────────────
     Error in `ser_permutation_vector(order, method = method$name)`: 'list' object cannot be coerced to type 'integer'
     Backtrace:
     β–ˆ
     1. └─protti::qc_sample_correlation(...) test-qc_functions.R:119:2
     2. └─dendextend::seriate_dendrogram(dendrogram, distance, method = "OLO")
     3. β”œβ”€seriation::seriate(...)
     4. └─seriation:::seriate.dist(...)
     5. β”œβ”€seriation::ser_permutation(ser_permutation_vector(order, method = method$name))
     6. └─seriation::ser_permutation_vector(order, method = method$name)
    
     [ FAIL 1 | WARN 0 | SKIP 0 | PASS 120 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: β€˜proDA’
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64

Version: 0.2.0
Check: examples
Result: ERROR
    Running examples in β€˜protti-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: qc_sample_correlation
    > ### Title: Correlation based hirachical clustering of samples
    > ### Aliases: qc_sample_correlation
    >
    > ### ** Examples
    >
    > set.seed(123) # Makes example reproducible
    >
    > # Create example data
    > data <- create_synthetic_data(
    + n_proteins = 100,
    + frac_change = 0.05,
    + n_replicates = 3,
    + n_conditions = 2,
    + method = "effect_random"
    + )
    >
    > # Create sample correlation heatmap
    > qc_sample_correlation(
    + data = data,
    + sample = sample,
    + grouping = peptide,
    + intensity_log2 = peptide_intensity_missing,
    + condition = condition
    + )
    Error in ser_permutation_vector(order, method = method$name) :
     'list' object cannot be coerced to type 'integer'
    Calls: qc_sample_correlation ... seriate.dist -> ser_permutation -> ser_permutation_vector
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK

Version: 0.2.0
Check: tests
Result: ERROR
     Running β€˜testthat.R’ [89s/109s]
    Running the tests in β€˜tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(protti)
     πŸ‘©πŸ½β€πŸ”¬ Welcome to protti version 0.2.0! πŸ‘¨πŸΌβ€πŸ’»
    
     πŸ”¬ Have fun analysing your data! πŸ’»
     >
     > test_check("protti")
     $`1`
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test-qc_functions.R:119:3): qc_sample_correlation works ──────────────
     Error in `ser_permutation_vector(order, method = method$name)`: 'list' object cannot be coerced to type 'integer'
     Backtrace:
     β–ˆ
     1. └─protti::qc_sample_correlation(...) test-qc_functions.R:119:2
     2. └─dendextend::seriate_dendrogram(dendrogram, distance, method = "OLO")
     3. β”œβ”€seriation::seriate(...)
     4. └─seriation:::seriate.dist(...)
     5. β”œβ”€seriation::ser_permutation(ser_permutation_vector(order, method = method$name))
     6. └─seriation::ser_permutation_vector(order, method = method$name)
    
     [ FAIL 1 | WARN 0 | SKIP 0 | PASS 120 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.0
Check: tests
Result: ERROR
     Running 'testthat.R'
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(protti)
     Welcome to protti version 0.2.0!
    
     Have fun analysing your data!
     >
     > test_check("protti")
     $`1`
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test-qc_functions.R:119:3): qc_sample_correlation works ──────────────
     Error in `ser_permutation_vector(order, method = method$name)`: 'list' object cannot be coerced to type 'integer'
     Backtrace:
     β–ˆ
     1. └─protti::qc_sample_correlation(...) test-qc_functions.R:119:2
     2. └─dendextend::seriate_dendrogram(dendrogram, distance, method = "OLO")
     3. β”œβ”€seriation::seriate(...)
     4. └─seriation:::seriate.dist(...)
     5. β”œβ”€seriation::ser_permutation(ser_permutation_vector(order, method = method$name))
     6. └─seriation::ser_permutation_vector(order, method = method$name)
    
     [ FAIL 1 | WARN 0 | SKIP 0 | PASS 120 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64-new-TK

Version: 0.2.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'proDA', 'STRINGdb'
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64