Last updated on 2019-05-08 16:46:34 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 2.47 | 81.02 | 83.49 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 1.89 | 64.26 | 66.15 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 92.25 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 93.79 | ERROR | |||
| r-patched-linux-x86_64 | 0.1.0 | 2.28 | 81.98 | 84.26 | ERROR | |
| r-patched-solaris-x86 | 0.1.0 | 141.30 | ERROR | |||
| r-release-linux-x86_64 | 0.1.0 | 2.30 | 81.00 | 83.30 | ERROR | |
| r-release-windows-ix86+x86_64 | 0.1.0 | 9.00 | 92.00 | 101.00 | ERROR | |
| r-release-osx-x86_64 | 0.1.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.1.0 | 7.00 | 68.00 | 75.00 | ERROR | |
| r-oldrel-osx-x86_64 | 0.1.0 | OK |
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [43s/45s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
-- 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ---------------
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
== testthat results ===========================================================
OK: 22 SKIPPED: 0 WARNINGS: 19 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
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’ [34s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
── 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ───────────────
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 22 SKIPPED: 0 WARNINGS: 19 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [45s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
── 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ───────────────
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 22 SKIPPED: 0 WARNINGS: 19 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
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’ [49s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
── 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ───────────────
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 22 SKIPPED: 0 WARNINGS: 19 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
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’ [44s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
── 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ───────────────
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 22 SKIPPED: 0 WARNINGS: 19 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [67s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
── 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ───────────────
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 22 SKIPPED: 0 WARNINGS: 19 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [43s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
── 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ───────────────
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 22 SKIPPED: 0 WARNINGS: 19 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
Error: testthat unit tests failed
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in 'cytominer-Ex.R' failed
The error most likely occurred in:
> ### Name: replicate_correlation
> ### Title: Measure replicate correlation of variables.
> ### Aliases: replicate_correlation
>
> ### ** Examples
>
> set.seed(123)
> x1 <- rnorm(10)
> x2 <- x1 + rnorm(10) / 100
> y1 <- rnorm(10)
> y2 <- y1 + rnorm(10) / 10
> z1 <- rnorm(10)
> z2 <- z1 + rnorm(10) / 1
>
> batch <- rep(rep(1:2, each=5), 2)
>
> treatment <- rep(1:10, 2)
>
> replicate_id <- rep(1:2, each=10)
>
> sample <-
+ tibble::data_frame(x = c(x1, x2), y = c(y1, y2), z = c(z1, z2),
+ Metadata_treatment = treatment,
+ Metadata_replicate_id = replicate_id,
+ Metadata_batch = batch)
>
> head(sample)
# A tibble: 6 x 6
x y z Metadata_treatment Metadata_replicate_id Metadata_batch
<dbl> <dbl> <dbl> <int> <int> <int>
1 -0.560 -1.07 -0.695 1 1 1
2 -0.230 -0.218 -0.208 2 1 1
3 1.56 -1.03 -1.27 3 1 1
4 0.0705 -0.729 2.17 4 1 1
5 0.129 -0.625 1.21 5 1 1
6 1.72 -1.69 -1.12 6 1 2
>
> # `replicate_correlation`` returns the median, min, and max
> # replicate correlation (across batches) per variable
> replicate_correlation(sample = sample,
+ variables = c("x", "y", "z"),
+ strata = c("Metadata_treatment"),
+ replicates = 2,
+ split_by = "Metadata_batch",
+ replicate_by = "Metadata_replicate_id",
+ cores = 1)
# A tibble: 3 x 4
variable median min max
<chr> <dbl> <dbl> <dbl>
1 x 1.000 1.000 1.000
2 y 0.996 0.993 0.999
3 z 0.627 0.290 0.964
>
>
>
>
> cleanEx()
Error: connections left open:
<-CRANwin.fb05.statistik.uni-dortmund.de:11968 (sockconn)
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
-- 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ---------------
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
== testthat results ===========================================================
OK: 18 SKIPPED: 2 WARNINGS: 10 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
Error: testthat unit tests failed
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(cytominer)
Attaching package: 'cytominer'
The following object is masked from 'package:stats':
aggregate
The following object is masked from 'package:base':
transform
>
> test_check("cytominer")
-- 1. Error: `aggregate` aggregates data (@test-aggregate.R#15) ---------------
near "(": syntax error
1: expect_equal(aggregate(population = data, variables = c("x", "y"), strata = c("g"),
operation = "median") %>% dplyr::collect(), data %>% dplyr::group_by(g) %>% dplyr::summarise_at(.funs = dplyr::funs(median),
.vars = c("x", "y"))) at testthat/test-aggregate.R:15
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: aggregate(population = data, variables = c("x", "y"), strata = c("g"), operation = "median") %>%
dplyr::collect()
5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6: eval(quote(`_fseq`(`_lhs`)), env, env)
7: eval(quote(`_fseq`(`_lhs`)), env, env)
8: `_fseq`(`_lhs`)
9: freduce(value, `_function_list`)
10: withVisible(function_list[[k]](value))
...
13: collect.tbl_sql(.)
14: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
15: db_collect.DBIConnection(x$src$con, sql, n = n, warn_incomplete = warn_incomplete)
16: dbSendQuery(con, sql)
17: dbSendQuery(con, sql)
18: .local(conn, statement, ...)
19: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr, statement), conn = conn,
bigint = conn@bigint)
20: initialize(value, ...)
21: initialize(value, ...)
22: result_create(conn@ptr, statement)
== testthat results ===========================================================
OK: 18 SKIPPED: 2 WARNINGS: 10 FAILED: 1
1. Error: `aggregate` aggregates data (@test-aggregate.R#15)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64