CRAN Package Check Results for Package lilikoi

Last updated on 2020-04-09 09:48:15 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.0	26.82	182.22	209.04	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.0	22.81	142.41	165.22	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.0			257.69	ERROR
r-devel-linux-x86_64-fedora-gcc	0.1.0			287.75	ERROR
r-devel-windows-ix86+x86_64	0.1.0	52.00	286.00	338.00	ERROR
r-devel-windows-ix86+x86_64-gcc8	0.1.0	50.00	175.00	225.00	ERROR
r-patched-linux-x86_64	0.1.0	24.68	179.03	203.71	ERROR
r-patched-osx-x86_64	0.1.0				ERROR
r-release-linux-x86_64	0.1.0	21.74	168.75	190.49	OK
r-release-windows-ix86+x86_64	0.1.0	56.00	279.00	335.00	OK
r-release-osx-x86_64	0.1.0				NOTE
r-oldrel-windows-ix86+x86_64	0.1.0	50.00	180.00	230.00	OK
r-oldrel-osx-x86_64	0.1.0				NOTE

Check Details

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in 'lilikoi-Ex.R' failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: lilikoi.get_pd_scores
    > ### Title: A lilikoi.get_pd_scores Function
    > ### Aliases: lilikoi.get_pd_scores
    >
    > ### ** Examples
    >
    > filename <- system.file("extdata", "plasma_breast_cancer.csv", package = "lilikoi")
    > data <- read.csv(file = filename, check.names = FALSE, row.names = 1)[, 1:20]
    > metaboliteNames <- colnames(data)[-1]
    > matches <- lilikoi.metab_to_pathway(metaboliteNames, "name")
    [1] "18 out of 19 Matched metabolites 90 %"
    [1] "1 out of 19 UnMatched metabolites 0 %"
    > PDSmatrix <- lilikoi.get_pd_scores(data, matches, lilikoi::data.smpdb[1:23,], maxit = 1)
    Warning in function_list[[i]](value) : NAs introduced by coercion
    robust_score_bydist. min_exp= 0 , min_std= 0
    Error in matrix(0, attempts, m) : invalid 'ncol' value (too large or NA)
    Calls: lilikoi.get_pd_scores -> .quantify_pathways_deregulation -> matrix
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [13s/14s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(lilikoi)
     >
     > test_check("lilikoi")
     [1] "18 out of 19 Matched metabolites 90 %"
     [1] "1 out of 19 UnMatched metabolites 0 %"
     robust_score_bydist. min_exp= 0 , min_std= 0
     -- 1. Error: full pipeline works (@test-all.r#12) -----------------------------
     invalid 'ncol' value (too large or NA)
     Backtrace:
     1. lilikoi::lilikoi.get_pd_scores(...)
     2. lilikoi:::.quantify_pathways_deregulation(...)
     3. base::matrix(0, attempts, m)

     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
     [1] "1 out of 4 Matched metabolites 60 %"
     [1] "3 out of 4 UnMatched metabolites 40 %"
     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "4 out of 5 Matched metabolites 80 %"
     [1] "1 out of 5 UnMatched metabolites 20 %"
     [1] "1 out of 1 Matched metabolites 100 %"
     [1] "0 out of 1 UnMatched metabolites 0 %"
     == testthat results ===========================================================
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: full pipeline works (@test-all.r#12)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [9s/12s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(lilikoi)
     >
     > test_check("lilikoi")
     [1] "18 out of 19 Matched metabolites 90 %"
     [1] "1 out of 19 UnMatched metabolites 0 %"
     robust_score_bydist. min_exp= 0 , min_std= 0
     ── 1. Error: full pipeline works (@test-all.r#12) ─────────────────────────────
     invalid 'ncol' value (too large or NA)
     Backtrace:
     1. lilikoi::lilikoi.get_pd_scores(...)
     2. lilikoi:::.quantify_pathways_deregulation(...)
     3. base::matrix(0, attempts, m)

     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
     [1] "1 out of 4 Matched metabolites 60 %"
     [1] "3 out of 4 UnMatched metabolites 40 %"
     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "4 out of 5 Matched metabolites 80 %"
     [1] "1 out of 5 UnMatched metabolites 20 %"
     [1] "1 out of 1 Matched metabolites 100 %"
     [1] "0 out of 1 UnMatched metabolites 0 %"
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: full pipeline works (@test-all.r#12)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.0
Check: installed package size
Result: NOTE
     installed size is 5.0Mb
     sub-directories of 1Mb or more:
     data 3.8Mb
     extdata 1.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-osx-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.1.0
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-osx-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.1.0
Check: data for non-ASCII characters
Result: NOTE
Note: found 3837 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-osx-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in ‘lilikoi-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: lilikoi.get_pd_scores
    > ### Title: A lilikoi.get_pd_scores Function
    > ### Aliases: lilikoi.get_pd_scores
    >
    > ### ** Examples
    >
    > filename <- system.file("extdata", "plasma_breast_cancer.csv", package = "lilikoi")
    > data <- read.csv(file = filename, check.names = FALSE, row.names = 1)[, 1:20]
    > metaboliteNames <- colnames(data)[-1]
    > matches <- lilikoi.metab_to_pathway(metaboliteNames, "name")
    [1] "18 out of 19 Matched metabolites 90 %"
    [1] "1 out of 19 UnMatched metabolites 0 %"
    > PDSmatrix <- lilikoi.get_pd_scores(data, matches, lilikoi::data.smpdb[1:23,], maxit = 1)
    Warning in function_list[[i]](value) : NAs introduced by coercion
    robust_score_bydist. min_exp= 0 , min_std= 0
    Error in matrix(0, attempts, m) : invalid 'ncol' value (too large or NA)
    Calls: lilikoi.get_pd_scores -> .quantify_pathways_deregulation -> matrix
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-osx-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [15s/16s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(lilikoi)
     >
     > test_check("lilikoi")
     [1] "18 out of 19 Matched metabolites 90 %"
     [1] "1 out of 19 UnMatched metabolites 0 %"
     robust_score_bydist. min_exp= 0 , min_std= 0
     ── 1. Error: full pipeline works (@test-all.r#12) ─────────────────────────────
     invalid 'ncol' value (too large or NA)
     Backtrace:
     1. lilikoi::lilikoi.get_pd_scores(...)
     2. lilikoi:::.quantify_pathways_deregulation(...)
     3. base::matrix(0, attempts, m)

     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
     [1] "1 out of 4 Matched metabolites 60 %"
     [1] "3 out of 4 UnMatched metabolites 40 %"
     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "4 out of 5 Matched metabolites 80 %"
     [1] "1 out of 5 UnMatched metabolites 20 %"
     [1] "1 out of 1 Matched metabolites 100 %"
     [1] "0 out of 1 UnMatched metabolites 0 %"
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: full pipeline works (@test-all.r#12)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [17s/22s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(lilikoi)
     >
     > test_check("lilikoi")
     [1] "18 out of 19 Matched metabolites 90 %"
     [1] "1 out of 19 UnMatched metabolites 0 %"
     robust_score_bydist. min_exp= 0 , min_std= 0
     ── 1. Error: full pipeline works (@test-all.r#12) ─────────────────────────────
     invalid 'ncol' value (too large or NA)
     Backtrace:
     1. lilikoi::lilikoi.get_pd_scores(...)
     2. lilikoi:::.quantify_pathways_deregulation(...)
     3. base::matrix(0, attempts, m)

     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
     [1] "1 out of 4 Matched metabolites 60 %"
     [1] "3 out of 4 UnMatched metabolites 40 %"
     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "4 out of 5 Matched metabolites 80 %"
     [1] "1 out of 5 UnMatched metabolites 20 %"
     [1] "1 out of 1 Matched metabolites 100 %"
     [1] "0 out of 1 UnMatched metabolites 0 %"
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: full pipeline works (@test-all.r#12)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [19s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(lilikoi)
     >
     > test_check("lilikoi")
     [1] "18 out of 19 Matched metabolites 90 %"
     [1] "1 out of 19 UnMatched metabolites 0 %"
     robust_score_bydist. min_exp= 0 , min_std= 0
     -- 1. Error: full pipeline works (@test-all.r#12) -----------------------------
     invalid 'ncol' value (too large or NA)
     Backtrace:
     1. lilikoi::lilikoi.get_pd_scores(...)
     2. lilikoi:::.quantify_pathways_deregulation(...)
     3. base::matrix(0, attempts, m)

     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
     [1] "1 out of 4 Matched metabolites 60 %"
     [1] "3 out of 4 UnMatched metabolites 40 %"
     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "4 out of 5 Matched metabolites 80 %"
     [1] "1 out of 5 UnMatched metabolites 20 %"
     [1] "1 out of 1 Matched metabolites 100 %"
     [1] "0 out of 1 UnMatched metabolites 0 %"
     == testthat results ===========================================================
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: full pipeline works (@test-all.r#12)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [12s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(lilikoi)
     >
     > test_check("lilikoi")
     [1] "18 out of 19 Matched metabolites 90 %"
     [1] "1 out of 19 UnMatched metabolites 0 %"
     robust_score_bydist. min_exp= 0 , min_std= 0
     -- 1. Error: full pipeline works (@test-all.r#12) -----------------------------
     invalid 'ncol' value (too large or NA)
     Backtrace:
     1. lilikoi::lilikoi.get_pd_scores(...)
     2. lilikoi:::.quantify_pathways_deregulation(...)
     3. base::matrix(0, attempts, m)

     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
     [1] "1 out of 4 Matched metabolites 60 %"
     [1] "3 out of 4 UnMatched metabolites 40 %"
     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "4 out of 5 Matched metabolites 80 %"
     [1] "1 out of 5 UnMatched metabolites 20 %"
     [1] "1 out of 1 Matched metabolites 100 %"
     [1] "0 out of 1 UnMatched metabolites 0 %"
     == testthat results ===========================================================
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: full pipeline works (@test-all.r#12)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [12s/13s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(lilikoi)
     >
     > test_check("lilikoi")
     [1] "18 out of 19 Matched metabolites 90 %"
     [1] "1 out of 19 UnMatched metabolites 0 %"
     robust_score_bydist. min_exp= 0 , min_std= 0
     ── 1. Error: full pipeline works (@test-all.r#12) ─────────────────────────────
     invalid 'ncol' value (too large or NA)
     Backtrace:
     1. lilikoi::lilikoi.get_pd_scores(...)
     2. lilikoi:::.quantify_pathways_deregulation(...)
     3. base::matrix(0, attempts, m)

     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
     [1] "1 out of 4 Matched metabolites 60 %"
     [1] "3 out of 4 UnMatched metabolites 40 %"
     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "4 out of 5 Matched metabolites 80 %"
     [1] "1 out of 5 UnMatched metabolites 20 %"
     [1] "1 out of 1 Matched metabolites 100 %"
     [1] "0 out of 1 UnMatched metabolites 0 %"
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: full pipeline works (@test-all.r#12)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [9s/14s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
     [1] "1 out of 4 Matched metabolites 60 %"
     [1] "3 out of 4 UnMatched metabolites 40 %"
     [1] "5 out of 5 Matched metabolites 100 %"
     [1] "0 out of 5 UnMatched metabolites 0 %"
     [1] "4 out of 5 Matched metabolites 80 %"
     [1] "1 out of 5 UnMatched metabolites 20 %"
     [1] "1 out of 1 Matched metabolites 100 %"
     [1] "0 out of 1 UnMatched metabolites 0 %"
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: full pipeline works (@test-all.r#12)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-osx-x86_64