Last updated on 2026-04-14 00:50:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.2 | 24.64 | 272.86 | 297.50 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.2 | 18.56 | 193.54 | 212.10 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.2 | 45.00 | 430.34 | 475.34 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.2 | 44.00 | 431.40 | 475.40 | ERROR | |
| r-devel-macos-arm64 | 0.2.2 | 7.00 | 69.00 | 76.00 | OK | |
| r-devel-windows-x86_64 | 0.2.2 | 28.00 | 252.00 | 280.00 | OK | |
| r-patched-linux-x86_64 | 0.2.2 | 25.40 | 221.45 | 246.85 | ERROR | |
| r-release-linux-x86_64 | 0.2.2 | 21.74 | 243.77 | 265.51 | OK | |
| r-release-macos-arm64 | 0.2.2 | OK | ||||
| r-release-macos-x86_64 | 0.2.2 | 16.00 | 244.00 | 260.00 | OK | |
| r-release-windows-x86_64 | 0.2.2 | 29.00 | 0.00 | 29.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.2 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.2 | 16.00 | 237.00 | 253.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.2 | 37.00 | 321.00 | 358.00 | OK |
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/73s]
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.
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
Saving _problems/test-protein_analysis-424.R
1 siginificantly differentially expressed proteins found.
Testing glm...
Testing rf...
Testing svmRadial...
Done!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-protein_analysis.R:419:3'): normalization works for cyclicloess ──
Expected `normalize_data(df_mp, method = "cyclicloess")` to equal `df_norm_c`.
Differences:
actual vs expected
[,1] [,2] [,3]
- actual[1, ] 10.086035 20.13598 70.205445
+ expected[1, ] 8.875947 21.90757 81.928810
- actual[2, ] 34.229368 34.59707 29.475138
+ expected[2, ] 35.918001 38.54878 35.918001
- actual[3, ] 20.748909 34.27025 17.497403
+ expected[3, ] 24.161291 24.16129 24.161291
- actual[4, ] 65.531947 57.33665 -6.608449
+ expected[4, ] 43.541565 43.54156 43.541565
- actual[5, ] 18.860601 11.89760 20.730052
+ expected[5, ] 17.339630 17.33963 17.339630
- actual[6, ] 42.446533 35.35054 45.603037
+ expected[6, ] 44.825964 44.82596 44.825964
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/80s]
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.
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
Saving _problems/test-protein_analysis-424.R
1 siginificantly differentially expressed proteins found.
Testing glm...
Testing rf...
Testing svmRadial...
Done!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-protein_analysis.R:419:3'): normalization works for cyclicloess ──
Expected `normalize_data(df_mp, method = "cyclicloess")` to equal `df_norm_c`.
Differences:
actual vs expected
[,1] [,2] [,3]
- actual[1, ] 10.086035 20.13598 70.205445
+ expected[1, ] 8.875947 21.90757 81.928810
- actual[2, ] 34.229368 34.59707 29.475138
+ expected[2, ] 35.918001 38.54878 35.918001
- actual[3, ] 20.748909 34.27025 17.497403
+ expected[3, ] 24.161291 24.16129 24.161291
- actual[4, ] 65.531947 57.33665 -6.608449
+ expected[4, ] 43.541565 43.54156 43.541565
- actual[5, ] 18.860601 11.89760 20.730052
+ expected[5, ] 17.339630 17.33963 17.339630
- actual[6, ] 42.446533 35.35054 45.603037
+ expected[6, ] 44.825964 44.82596 44.825964
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in ‘promor-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: heatmap_na
> ### Title: Visualize missing data
> ### Aliases: heatmap_na
>
> ### ** Examples
>
> ## Generate a raw_df object with default settings. No technical replicates.
> raw_df <- create_df(
+ prot_groups = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt",
+ exp_design = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/ed1.txt"
+ )
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
URL 'https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt': Timeout of 60 seconds was reached
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
cannot read from connection
Calls: create_df -> read.csv -> read.table -> scan
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
feature_plot 6.206 0.088 7.539
corr_plot 1.098 0.151 30.951
aver_techreps 1.046 0.088 32.244
Flavor: r-patched-linux-x86_64