POTENTIAL BUG: partial match of 'Z' to 'Z1'

[HenrikBengtsson]

Not sure if testthat does it automatically, but I have the following in my ~/.Rprofile:

options(warnPartialMatchArgs = TRUE, warnPartialMatchAttr = TRUE, warnPartialMatchDollar = TRUE)

and then I get lots of warnings:

> devtools::test()
Loading c3co
Loading required package: testthat

Attaching package: 'testthat'

The following object is masked from 'package:purrr':

    is_null

Warning: S3 method 'segmentData.list' was declared in NAMESPACE but not found
Testing c3co
Warning: `encoding` is deprecated; all files now assumed to be UTF-8
✔ | OK F W S | Context
✔ | 42       | Construction of subclones [0.6 s]
✔ |  0   10   | c3co test [5.1 s]
──────────────────────────────────────────────────────────────────────────────────
test_c3co.R:38: warning: c3co terminates on C1,C2
partial match of 'coefficient' to 'coefficients'

test_c3co.R:38: warning: c3co terminates on C1,C2
partial match of 'bkp' to 'bkpList'

test_c3co.R:38: warning: c3co terminates on C1,C2
partial match of 'bkp' to 'bkpList'

test_c3co.R:38: warning: c3co terminates on C1,C2
For model with 2 features, some components in minor latent profiles are larger than matched components in major latent profiles

test_c3co.R:38: warning: c3co terminates on C1,C2
For model with 4 features, some components in minor latent profiles are larger than matched components in major latent profiles

test_c3co.R:38: warning: c3co terminates on C1,C2
For model with 5 features, some components in minor latent profiles are larger than matched components in major latent profiles

test_c3co.R:38: warning: c3co terminates on C1,C2
For model with 6 features, some components in minor latent profiles are larger than matched components in major latent profiles

test_c3co.R:45: warning: c3co terminates on TCN
partial match of 'coefficient' to 'coefficients'

test_c3co.R:45: warning: c3co terminates on TCN
partial match of 'bkp' to 'bkpList'

test_c3co.R:45: warning: c3co terminates on TCN
partial match of 'bkp' to 'bkpList'
──────────────────────────────────────────────────────────────────────────────────
✔ | 20       | Toy data generation
✔ | 32   15   | Initialization of the latent features [95.9 s]
──────────────────────────────────────────────────────────────────────────────────
test_initializeZ.R:16: warning: (unknown)
partial match of 'coefficient' to 'coefficients'

test_initializeZ.R:16: warning: (unknown)
partial match of 'bkp' to 'bkpList'

test_initializeZ.R:16: warning: (unknown)
partial match of 'bkp' to 'bkpList'

test_initializeZ.R:36: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:38: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:39: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:36: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:38: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:39: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:36: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:38: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:39: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:36: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:38: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

test_initializeZ.R:39: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'
──────────────────────────────────────────────────────────────────────────────────
⠋ |  0 1     | c3co test on PSCBS data[1] "Segmented data is provided, skip segment step"
✖ |  0 1   1 | c3co test on PSCBS data [55.7 s]
──────────────────────────────────────────────────────────────────────────────────
test_PSCBS.R:7: error: Produce (C1,C2) segmentation from PSCBS locus-level data
argument is not interpretable as logical
1: PSCBSwrapper(PSCBSdata, stat = "C1C2") at /home/hb/repositories/c3co/tests/testthat/test_PSCBS.R:7

test_PSCBS.R:16: skip: c3co terminates on PSCBS locus-level data
Empty test
──────────────────────────────────────────────────────────────────────────────────
✔ | 40       | Construction of weight matrices
⠹ | 40   3   | Construction of weight matrices
══ Results ═══════════════════════════════════════════════════════════════════════
Duration: 158.6 s

OK:       134
Failed:   1
Warnings: 28
Skipped:  1

I've already reported on some of these:

• https://github.com/mpierrejean/jointseg/issues/7
• https://github.com/mpierrejean/jointseg/issues/8

but the:

test_initializeZ.R:39: warning: output of initializeZ has correct dimensions and contents
partial match of 'Z' to 'Z1'

ones looks potentially concerning.

[HenrikBengtsson]

Turns out it was a partial element name matching in the test script itself - not the c3co code.