Last updated on 2025-10-31 07:51:54 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.1 | 23.26 | 236.29 | 259.55 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.1 | 18.02 | 162.05 | 180.07 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.1 | 55.00 | 348.94 | 403.94 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.1 | 106.00 | 315.59 | 421.59 | ERROR | |
| r-devel-windows-x86_64 | 0.2.1 | 25.00 | 217.00 | 242.00 | NOTE | |
| r-patched-linux-x86_64 | 0.2.1 | 21.95 | 225.10 | 247.05 | ERROR | |
| r-release-linux-x86_64 | 0.2.1 | 21.63 | 221.52 | 243.15 | NOTE | |
| r-release-macos-arm64 | 0.2.1 | 11.00 | 103.00 | 114.00 | NOTE | |
| r-release-macos-x86_64 | 0.2.1 | 17.00 | 186.00 | 203.00 | NOTE | |
| r-release-windows-x86_64 | 0.2.1 | 25.00 | 219.00 | 244.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.2.1 | 9.00 | 103.00 | 112.00 | NOTE | |
| r-oldrel-macos-x86_64 | 0.2.1 | 14.00 | 153.00 | 167.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.2.1 | 33.00 | 286.00 | 319.00 | NOTE |
Version: 0.2.1
Check: Rd files
Result: NOTE
checkRd: (-1) impute_plot.Rd:32: Lost braces; missing escapes or markup?
32 | \item{global}{Logical. If \code{TRUE} ({default}), a global density plot is
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(promor)
>
> test_check("promor")
0 empty row(s) removed.
2 empty column(s) removed.
1 protein(s) (rows) only identified by site removed.
4 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
4 proteins with higher than 33% NAs in at least one group removed.
0 empty row(s) removed.
4 empty column(s) removed.
10 protein contaminant(s) (rows) removed.
0 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
missForest iteration 1 in progress...done!
estimated error(s): 1.04084
difference(s): 0.0005251996
time: 0.056 seconds
missForest iteration 2 in progress...done!
estimated error(s): 1.067432
difference(s): 0.002956259
time: 0.055 seconds
b c b c
20 22 39 82
a c a c
11 22 83 82
a b a b
11 20 83 39
change in estimate: 0.02415548
change in estimate: 0.02101209
change in estimate: 0.01821531
change in estimate: 0.0157772
change in estimate: 0.01367284
change in estimate: 0.01186459
change in estimate: 0.01031291
change in estimate: 0.008980791
1 siginificantly differentially expressed proteins found.
Testing glm...
Testing rf...
Testing svmRadial...
Done!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-protein_analysis.R:336:3'): impute_na works for rf ───────────
impute_na(df, method = "RF", seed = 327) (`actual`) not equal to `df_rf` (`expected`).
actual vs expected
a b c
- actual[1, ] 12.00000 29.33333 82.000
+ expected[1, ] 12.00000 26.60000 82.000
- actual[2, ] 34.00000 29.33333 40.000
+ expected[2, ] 34.00000 32.15000 40.000
actual[3, ] 11.00000 39.00000 22.000
- actual[4, ] 83.00000 29.00000 50.350
+ expected[4, ] 83.00000 29.00000 53.125
- actual[5, ] 42.09000 20.00000 50.350
+ expected[5, ] 62.16333 20.00000 66.025
- actual[6, ] 67.00000 29.33333 70.000
+ expected[6, ] 67.00000 22.30000 70.000
`actual$a[2:6]`: 34.0 11.0 83.0 42.1 67.0
`expected$a[2:6]`: 34.0 11.0 83.0 62.2 67.0
`actual$b`: 29.3 29.3 39.0 29.0 20.0 29.3
`expected$b`: 26.6 32.1 39.0 29.0 20.0 22.3
`actual$c`: 82.0 40.0 22.0 50.4 50.4 70.0
`expected$c`: 82.0 40.0 22.0 53.1 66.0 70.0
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-protein_analysis.R:336:3
2. │ └─base::withCallingHandlers(...)
3. └─testthat::expect_equal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(promor)
>
> test_check("promor")
0 empty row(s) removed.
2 empty column(s) removed.
1 protein(s) (rows) only identified by site removed.
4 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
4 proteins with higher than 33% NAs in at least one group removed.
0 empty row(s) removed.
4 empty column(s) removed.
10 protein contaminant(s) (rows) removed.
0 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
missForest iteration 1 in progress...done!
estimated error(s): 1.04084
difference(s): 0.0005251996
time: 0.054 seconds
missForest iteration 2 in progress...done!
estimated error(s): 1.067432
difference(s): 0.002956259
time: 0.063 seconds
b c b c
20 22 39 82
a c a c
11 22 83 82
a b a b
11 20 83 39
change in estimate: 0.02415548
change in estimate: 0.02101209
change in estimate: 0.01821531
change in estimate: 0.0157772
change in estimate: 0.01367284
change in estimate: 0.01186459
change in estimate: 0.01031291
change in estimate: 0.008980791
1 siginificantly differentially expressed proteins found.
Testing glm...
Testing rf...
Testing svmRadial...
Done!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-protein_analysis.R:336:3'): impute_na works for rf ───────────
impute_na(df, method = "RF", seed = 327) (`actual`) not equal to `df_rf` (`expected`).
actual vs expected
a b c
- actual[1, ] 12.00000 29.33333 82.000
+ expected[1, ] 12.00000 26.60000 82.000
- actual[2, ] 34.00000 29.33333 40.000
+ expected[2, ] 34.00000 32.15000 40.000
actual[3, ] 11.00000 39.00000 22.000
- actual[4, ] 83.00000 29.00000 50.350
+ expected[4, ] 83.00000 29.00000 53.125
- actual[5, ] 42.09000 20.00000 50.350
+ expected[5, ] 62.16333 20.00000 66.025
- actual[6, ] 67.00000 29.33333 70.000
+ expected[6, ] 67.00000 22.30000 70.000
`actual$a[2:6]`: 34.0 11.0 83.0 42.1 67.0
`expected$a[2:6]`: 34.0 11.0 83.0 62.2 67.0
`actual$b`: 29.3 29.3 39.0 29.0 20.0 29.3
`expected$b`: 26.6 32.1 39.0 29.0 20.0 22.3
`actual$c`: 82.0 40.0 22.0 50.4 50.4 70.0
`expected$c`: 82.0 40.0 22.0 53.1 66.0 70.0
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-protein_analysis.R:336:3
2. │ └─base::withCallingHandlers(...)
3. └─testthat::expect_equal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [24s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(promor)
>
> test_check("promor")
0 empty row(s) removed.
2 empty column(s) removed.
1 protein(s) (rows) only identified by site removed.
4 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
4 proteins with higher than 33% NAs in at least one group removed.
0 empty row(s) removed.
4 empty column(s) removed.
10 protein contaminant(s) (rows) removed.
0 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
missForest iteration 1 in progress...done!
estimated error(s): 1.104733
difference(s): 0.000166978
time: 0.084 seconds
missForest iteration 2 in progress...done!
estimated error(s): 1.021219
difference(s): 0.002309109
time: 0.048 seconds
b c b c
20 22 39 82
a c a c
11 22 83 82
a b a b
11 20 83 39
change in estimate: 0.02415548
change in estimate: 0.02101209
change in estimate: 0.01821531
change in estimate: 0.0157772
change in estimate: 0.01367284
change in estimate: 0.01186459
change in estimate: 0.01031291
change in estimate: 0.008980791
1 siginificantly differentially expressed proteins found.
Testing glm...
Testing rf...
Testing svmRadial...
Done!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-protein_analysis.R:336:3'): impute_na works for rf ───────────
impute_na(df, method = "RF", seed = 327) (`actual`) not equal to `df_rf` (`expected`).
actual vs expected
a b c
- actual[1, ] 12.00000 28.70 82.000
+ expected[1, ] 12.00000 26.60 82.000
- actual[2, ] 34.00000 28.70 40.000
+ expected[2, ] 34.00000 32.15 40.000
actual[3, ] 11.00000 39.00 22.000
- actual[4, ] 83.00000 29.00 52.150
+ expected[4, ] 83.00000 29.00 53.125
- actual[5, ] 42.69000 20.00 52.150
+ expected[5, ] 62.16333 20.00 66.025
- actual[6, ] 67.00000 28.70 70.000
+ expected[6, ] 67.00000 22.30 70.000
`actual$a[2:6]`: 34.0 11.0 83.0 42.7 67.0
`expected$a[2:6]`: 34.0 11.0 83.0 62.2 67.0
`actual$b`: 28.7 28.7 39.0 29.0 20.0 28.7
`expected$b`: 26.6 32.1 39.0 29.0 20.0 22.3
`actual$c`: 82.00 40.00 22.00 52.15 52.15 70.00
`expected$c`: 82.00 40.00 22.00 53.12 66.03 70.00
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-protein_analysis.R:336:3
2. │ └─base::withCallingHandlers(...)
3. └─testthat::expect_equal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(promor)
>
> test_check("promor")
0 empty row(s) removed.
2 empty column(s) removed.
1 protein(s) (rows) only identified by site removed.
4 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
4 proteins with higher than 33% NAs in at least one group removed.
0 empty row(s) removed.
4 empty column(s) removed.
10 protein contaminant(s) (rows) removed.
0 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
missForest iteration 1 in progress...done!
estimated error(s): 1.04084
difference(s): 0.0005251996
time: 0.117 seconds
missForest iteration 2 in progress...done!
estimated error(s): 1.067432
difference(s): 0.002956259
time: 0.054 seconds
b c b c
20 22 39 82
a c a c
11 22 83 82
a b a b
11 20 83 39
change in estimate: 0.02415548
change in estimate: 0.02101209
change in estimate: 0.01821531
change in estimate: 0.0157772
change in estimate: 0.01367284
change in estimate: 0.01186459
change in estimate: 0.01031291
change in estimate: 0.008980791
1 siginificantly differentially expressed proteins found.
Testing glm...
Testing rf...
Testing svmRadial...
Done!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-protein_analysis.R:336:3'): impute_na works for rf ───────────
impute_na(df, method = "RF", seed = 327) (`actual`) not equal to `df_rf` (`expected`).
actual vs expected
a b c
- actual[1, ] 12.00000 29.33333 82.000
+ expected[1, ] 12.00000 26.60000 82.000
- actual[2, ] 34.00000 29.33333 40.000
+ expected[2, ] 34.00000 32.15000 40.000
actual[3, ] 11.00000 39.00000 22.000
- actual[4, ] 83.00000 29.00000 50.350
+ expected[4, ] 83.00000 29.00000 53.125
- actual[5, ] 42.09000 20.00000 50.350
+ expected[5, ] 62.16333 20.00000 66.025
- actual[6, ] 67.00000 29.33333 70.000
+ expected[6, ] 67.00000 22.30000 70.000
`actual$a[2:6]`: 34.0 11.0 83.0 42.1 67.0
`expected$a[2:6]`: 34.0 11.0 83.0 62.2 67.0
`actual$b`: 29.3 29.3 39.0 29.0 20.0 29.3
`expected$b`: 26.6 32.1 39.0 29.0 20.0 22.3
`actual$c`: 82.0 40.0 22.0 50.4 50.4 70.0
`expected$c`: 82.0 40.0 22.0 53.1 66.0 70.0
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-protein_analysis.R:336:3
2. │ └─base::withCallingHandlers(...)
3. └─testthat::expect_equal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(promor)
>
> test_check("promor")
0 empty row(s) removed.
2 empty column(s) removed.
1 protein(s) (rows) only identified by site removed.
4 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
4 proteins with higher than 33% NAs in at least one group removed.
0 empty row(s) removed.
4 empty column(s) removed.
10 protein contaminant(s) (rows) removed.
0 protein(s) identified by 2 or fewer unique peptides removed.
Zeros have been replaced with NAs.
Data have been log-transformed.
missForest iteration 1 in progress...done!
estimated error(s): 1.04084
difference(s): 0.0005251996
time: 0.073 seconds
missForest iteration 2 in progress...done!
estimated error(s): 1.067432
difference(s): 0.002956259
time: 0.055 seconds
b c b c
20 22 39 82
a c a c
11 22 83 82
a b a b
11 20 83 39
change in estimate: 0.02415548
change in estimate: 0.02101209
change in estimate: 0.01821531
change in estimate: 0.0157772
change in estimate: 0.01367284
change in estimate: 0.01186459
change in estimate: 0.01031291
change in estimate: 0.008980791
1 siginificantly differentially expressed proteins found.
Testing glm...
Testing rf...
Testing svmRadial...
Done!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-protein_analysis.R:336:3'): impute_na works for rf ───────────
impute_na(df, method = "RF", seed = 327) (`actual`) not equal to `df_rf` (`expected`).
actual vs expected
a b c
- actual[1, ] 12.00000 29.33333 82.000
+ expected[1, ] 12.00000 26.60000 82.000
- actual[2, ] 34.00000 29.33333 40.000
+ expected[2, ] 34.00000 32.15000 40.000
actual[3, ] 11.00000 39.00000 22.000
- actual[4, ] 83.00000 29.00000 50.350
+ expected[4, ] 83.00000 29.00000 53.125
- actual[5, ] 42.09000 20.00000 50.350
+ expected[5, ] 62.16333 20.00000 66.025
- actual[6, ] 67.00000 29.33333 70.000
+ expected[6, ] 67.00000 22.30000 70.000
`actual$a[2:6]`: 34.0 11.0 83.0 42.1 67.0
`expected$a[2:6]`: 34.0 11.0 83.0 62.2 67.0
`actual$b`: 29.3 29.3 39.0 29.0 20.0 29.3
`expected$b`: 26.6 32.1 39.0 29.0 20.0 22.3
`actual$c`: 82.0 40.0 22.0 50.4 50.4 70.0
`expected$c`: 82.0 40.0 22.0 53.1 66.0 70.0
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-protein_analysis.R:336:3
2. │ └─base::withCallingHandlers(...)
3. └─testthat::expect_equal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64