Last updated on 2022-02-22 16:49:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.1 | 20.51 | 169.01 | 189.52 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.1 | 16.74 | 124.01 | 140.75 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.1 | 229.27 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.1 | 231.45 | ERROR | |||
| r-devel-windows-x86_64-new-UL | 0.2.1 | 90.00 | 312.00 | 402.00 | OK | |
| r-devel-windows-x86_64-new-TK | 0.2.1 | ERROR | ||||
| r-patched-linux-x86_64 | 0.2.1 | 16.20 | 156.14 | 172.34 | ERROR | |
| r-release-linux-x86_64 | 0.2.1 | 11.86 | 156.27 | 168.13 | ERROR | |
| r-release-macos-arm64 | 0.2.1 | NOTE | ||||
| r-release-macos-x86_64 | 0.2.1 | OK | ||||
| r-release-windows-ix86+x86_64 | 0.2.1 | 37.00 | 306.00 | 343.00 | OK | |
| r-oldrel-macos-x86_64 | 0.2.1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.2.1 | 37.00 | 319.00 | 356.00 | OK |
Version: 0.2.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'iq'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2.1
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: calculate_protein_abundance
> ### Title: Label-free protein quantification
> ### Aliases: calculate_protein_abundance
>
> ### ** Examples
>
> # Create example data
> data <- data.frame(
+ sample = c(
+ rep("S1", 6),
+ rep("S2", 6),
+ rep("S1", 2),
+ rep("S2", 2)
+ ),
+ protein_id = c(
+ rep("P1", 12),
+ rep("P2", 4)
+ ),
+ precursor = c(
+ rep(c("A1", "A2", "B1", "B2", "C1", "D1"), 2),
+ rep(c("E1", "F1"), 2)
+ ),
+ peptide = c(
+ rep(c("A", "A", "B", "B", "C", "D"), 2),
+ rep(c("E", "F"), 2)
+ ),
+ intensity = c(
+ rnorm(n = 6, mean = 15, sd = 2),
+ rnorm(n = 6, mean = 21, sd = 1),
+ rnorm(n = 2, mean = 15, sd = 1),
+ rnorm(n = 2, mean = 15, sd = 2)
+ )
+ )
>
> data
sample protein_id precursor peptide intensity
1 S1 P1 A1 A 13.74709
2 S1 P1 A2 A 15.36729
3 S1 P1 B1 B 13.32874
4 S1 P1 B2 B 18.19056
5 S1 P1 C1 C 15.65902
6 S1 P1 D1 D 13.35906
7 S2 P1 A1 A 21.48743
8 S2 P1 A2 A 21.73832
9 S2 P1 B1 B 21.57578
10 S2 P1 B2 B 20.69461
11 S2 P1 C1 C 22.51178
12 S2 P1 D1 D 21.38984
13 S1 P2 E1 E 14.37876
14 S1 P2 F1 F 12.78530
15 S2 P2 E1 E 17.24986
16 S2 P2 F1 F 14.91013
>
> # Calculate protein abundances
> protein_abundance <- calculate_protein_abundance(
+ data,
+ sample = sample,
+ protein_id = protein_id,
+ precursor = precursor,
+ peptide = peptide,
+ intensity_log2 = intensity,
+ method = "iq",
+ for_plot = FALSE
+ )
Error: Package "iq" is needed for this function to work. Please install it.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2.1
Check: tests
Result: ERROR
Running 'testthat.R' [25s/30s]
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 0.2.1! <U+0001F468><U+0001F3FC><U+200D><U+0001F4BB>
<U+0001F52C> Have fun analysing your data! <U+0001F4BB>
>
> test_check("protti")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
== Failed tests ================================================================
-- Error (test-workflow.R:152:1): (code run outside of `test_that()`) ----------
Error: Package "iq" is needed for this function to work. Please install it.
Backtrace:
x
1. \-protti::calculate_protein_abundance(...) at test-workflow.R:152:0
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [18s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(protti)
👩🏽🔬 Welcome to protti version 0.2.1! 👨🏼💻
🔬 Have fun analysing your data! 💻
>
> test_check("protti")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-workflow.R:152:1): (code run outside of `test_that()`) ──────────
Error: Package "iq" is needed for this function to work. Please install it.
Backtrace:
▆
1. └─protti::calculate_protein_abundance(...) at test-workflow.R:152:0
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.1
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'proDA', 'iq'
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.1
Check: examples
Result: ERROR
Running examples in ‘protti-Ex.R’ failed
The error most likely occurred in:
> ### Name: calculate_protein_abundance
> ### Title: Label-free protein quantification
> ### Aliases: calculate_protein_abundance
>
> ### ** Examples
>
> # Create example data
> data <- data.frame(
+ sample = c(
+ rep("S1", 6),
+ rep("S2", 6),
+ rep("S1", 2),
+ rep("S2", 2)
+ ),
+ protein_id = c(
+ rep("P1", 12),
+ rep("P2", 4)
+ ),
+ precursor = c(
+ rep(c("A1", "A2", "B1", "B2", "C1", "D1"), 2),
+ rep(c("E1", "F1"), 2)
+ ),
+ peptide = c(
+ rep(c("A", "A", "B", "B", "C", "D"), 2),
+ rep(c("E", "F"), 2)
+ ),
+ intensity = c(
+ rnorm(n = 6, mean = 15, sd = 2),
+ rnorm(n = 6, mean = 21, sd = 1),
+ rnorm(n = 2, mean = 15, sd = 1),
+ rnorm(n = 2, mean = 15, sd = 2)
+ )
+ )
>
> data
sample protein_id precursor peptide intensity
1 S1 P1 A1 A 13.74709
2 S1 P1 A2 A 15.36729
3 S1 P1 B1 B 13.32874
4 S1 P1 B2 B 18.19056
5 S1 P1 C1 C 15.65902
6 S1 P1 D1 D 13.35906
7 S2 P1 A1 A 21.48743
8 S2 P1 A2 A 21.73832
9 S2 P1 B1 B 21.57578
10 S2 P1 B2 B 20.69461
11 S2 P1 C1 C 22.51178
12 S2 P1 D1 D 21.38984
13 S1 P2 E1 E 14.37876
14 S1 P2 F1 F 12.78530
15 S2 P2 E1 E 17.24986
16 S2 P2 F1 F 14.91013
>
> # Calculate protein abundances
> protein_abundance <- calculate_protein_abundance(
+ data,
+ sample = sample,
+ protein_id = protein_id,
+ precursor = precursor,
+ peptide = peptide,
+ intensity_log2 = intensity,
+ method = "iq",
+ for_plot = FALSE
+ )
Error: Package "iq" is needed for this function to work. Please install it.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [29s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(protti)
👩🏽🔬 Welcome to protti version 0.2.1! 👨🏼💻
🔬 Have fun analysing your data! 💻
>
> test_check("protti")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-workflow.R:152:1): (code run outside of `test_that()`) ──────────
Error: Package "iq" is needed for this function to work. Please install it.
Backtrace:
▆
1. └─protti::calculate_protein_abundance(...) at test-workflow.R:152:0
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [31s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(protti)
👩🏽🔬 Welcome to protti version 0.2.1! 👨🏼💻
🔬 Have fun analysing your data! 💻
>
> test_check("protti")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-workflow.R:152:1): (code run outside of `test_that()`) ──────────
Error: Package "iq" is needed for this function to work. Please install it.
Backtrace:
▆
1. └─protti::calculate_protein_abundance(...) at test-workflow.R:152:0
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.1
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 0.2.1!
Have fun analysing your data!
>
> test_check("protti")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-workflow.R:152:1): (code run outside of `test_that()`) ──────────
Error: Package "iq" is needed for this function to work. Please install it.
Backtrace:
▆
1. └─protti::calculate_protein_abundance(...) at test-workflow.R:152:0
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64-new-TK
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(protti)
👩🏽🔬 Welcome to protti version 0.2.1! 👨🏼💻
🔬 Have fun analysing your data! 💻
>
> test_check("protti")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-workflow.R:152:1): (code run outside of `test_that()`) ──────────
Error: Package "iq" is needed for this function to work. Please install it.
Backtrace:
▆
1. └─protti::calculate_protein_abundance(...) at test-workflow.R:152:0
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘proDA’
Flavor: r-release-macos-arm64
Version: 0.2.1
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'proDA', 'STRINGdb'
Flavor: r-oldrel-macos-x86_64