Last updated on 2024-11-09 01:50:04 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| lava | 1 | 12 | |
| mets | 1 | 6 | 6 |
| targeted | 1 | 4 | 8 |
Current CRAN status: ERROR: 1, OK: 12
Version: 1.8.0
Check: examples
Result: ERROR
Running examples in ‘lava-Ex.R’ failed
The error most likely occurred in:
> ### Name: Missing
> ### Title: Missing value generator
> ### Aliases: Missing Missing, Missing<-
>
> ### ** Examples
>
> library(lava)
> set.seed(17)
> m <- lvm(y0~x01+x02+x03)
> m <- Missing(m,formula=x1~x01,Rformula=R1~0.3*x02+-0.7*x01,p=0.4)
> sim(m,10)
y0 x01 x02 x03 R1 x1
1 -0.3307614 1.18078924 0.6810276 -1.17756957 0 NA
2 -1.0786445 0.64319207 -0.6820334 -0.96016651 0 NA
3 -0.5398741 1.29532187 -0.7232567 -0.87895224 0 NA
4 -2.5119604 0.18791807 1.6735260 -3.55613648 1 0.1879181
5 0.3507905 1.59120510 -0.5957556 -1.41674984 0 NA
6 0.4902836 -0.05517906 1.1598438 -0.44876927 0 NA
7 1.1528003 0.83847112 0.1174224 -0.77596771 1 0.8384711
8 1.3032974 0.15937013 0.2592214 -0.83182805 0 NA
9 1.3153836 0.62595440 0.3823621 0.05183012 1 0.6259544
10 -0.3278672 0.63358473 -0.7114817 -0.61655131 0 NA
>
>
> m <- lvm(y~1)
Error in cbind(idxM, pidxM) : cannot get data pointer of 'NULL' objects
Calls: lvm ... intercept<- -> intercept<-.lvm -> reindex -> mat.lvm -> cbind
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.8.0
Check: tests
Result: ERROR
Running ‘test-all.R’ [41s/51s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> #library("lava")
> suppressPackageStartupMessages(library("testthat"))
> test_check("lava")
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
0: 13.081250: 0.200620 0.00000 0.337259
1: 7.9524457: 0.272131 0.575626 1.15184
2: 7.4635337: 0.132261 0.763214 0.929738
3: 7.0359771: 0.0594089 0.733914 0.616824
4: 6.9865362: 0.0794124 0.756603 0.558204
5: 6.9757752: 0.0833126 0.759329 0.492413
6: 6.9738107: 0.0806668 0.756413 0.513241
7: 6.9737419: 0.0827969 0.758414 0.510545
8: 6.9737365: 0.0806693 0.757663 0.508982
9: 6.9737257: 0.0819960 0.757150 0.509933
10: 6.9737242: 0.0817930 0.757623 0.509977
11: 6.9737241: 0.0816735 0.757610 0.509971
12: 6.9737241: 0.0816798 0.757610 0.509973
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 173 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-constrain.R:51:5'): Non-linear in exogenous variables ──────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(y[m] ~ 1) at test-constrain.R:51:5
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`intercept<-`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
6. └─lava:::`intercept<-.lvm`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
7. └─lava::reindex(object)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
── Error ('test-constrain.R:66:5'): Probit constraints ─────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. ├─lava::`ordinal<-`(...) at test-constrain.R:66:5
2. └─lava:::`ordinal<-.lvm`(...)
3. ├─lava::ordinal(x, value, ...)
4. └─lava:::ordinal.lvm(x, value, ...)
5. ├─lava::`intfix<-`(`*tmp*`, var[i], NULL, value = 0)
6. └─lava:::`intfix<-.lvm`(`*tmp*`, var[i], NULL, value = 0)
7. ├─lava::`intercept<-`(`*tmp*`, ..., value = value)
8. └─lava:::`intercept<-.lvm`(`*tmp*`, ..., value = value)
9. └─lava::reindex(object)
10. └─lava:::mat.lvm(x, res)
11. └─base::cbind(idxM, pidxM)
── Error ('test-constrain.R:92:3'): Multiple group constraints II ──────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(~bw.1 + bw.2) at test-constrain.R:92:3
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`exogenous<-`(...)
6. └─lava:::`exogenous<-.lvm`(...)
7. └─lava::reindex(x)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
── Error ('test-inference.R:47:5'): IV-estimator ───────────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. ├─lava::estimate(m, d, estimator = "iv") at test-inference.R:47:5
2. └─lava:::estimate.lvm(m, d, estimator = "iv")
3. ├─base::do.call(...)
4. └─lava:::IV_objective.lvm(x = `<lvm>`, data = `<df[,4]>`, control = `<list>`)
5. └─lava:::IV2(x, data, ...)
6. ├─lava::parfix(m, idx, p)
7. └─lava:::parfix.lvm(m, idx, p)
8. └─lava::reindex(object)
9. └─lava:::mat.lvm(x, res)
10. └─base::cbind(idxM, pidxM)
── Error ('test-inference.R:118:5'): modelsearch and GoF ───────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. ├─lava::estimate(lvm(c(y1, y2) ~ 1, y1 ~ x), d) at test-inference.R:118:5
2. └─lava::lvm(c(y1, y2) ~ 1, y1 ~ x)
3. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
4. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
5. └─lava::procformula(object, value, ...)
6. ├─lava::`intercept<-`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
7. └─lava:::`intercept<-.lvm`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
8. └─lava::reindex(object)
9. └─lava:::mat.lvm(x, res)
10. └─base::cbind(idxM, pidxM)
── Error ('test-inference.R:255:5'): Prediction with missing data, random intercept ──
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(c(y1, y2, y3) ~ u[0]) at test-inference.R:255:5
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`intercept<-`(...)
6. └─lava:::`intercept<-.lvm`(...)
7. └─lava::reindex(object)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
── Error ('test-inference.R:323:5'): Random slope model ────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(c(y1[0:v], y2[0:v], y3[0:v]) ~ 1 * u) at test-inference.R:323:5
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`intercept<-`(...)
6. └─lava:::`intercept<-.lvm`(...)
7. └─lava::reindex(object)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
── Error ('test-model.R:4:5'): Basic model building blocks ─────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(y[m] ~ x) at test-model.R:4:5
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`intercept<-`(...)
6. └─lava:::`intercept<-.lvm`(...)
7. └─lava::reindex(object)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
── Error ('test-model.R:88:5'): Graph attributes ───────────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::graph2lvm(g1) at test-model.R:88:5
2. └─lava::lvm(graph::nodes(g), debug = debug, messages = messages)
3. ├─lava::addvar(res, myvar, messages = messages)
4. └─lava:::addvar.lvm(res, myvar, messages = messages)
5. └─lava::reindex(x)
6. └─lava:::mat.lvm(x, res)
7. └─base::cbind(idxM, pidxM)
── Error ('test-model.R:119:5'): Categorical variables ─────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::`categorical<-`(`*tmp*`, K = 3, p = c(0.1, 0.5), value = `<formula>`) at test-model.R:119:5
2. └─lava::categorical(x, value, ...)
3. ├─lava::`ordinal<-`(...)
4. └─lava:::`ordinal<-.lvm`(...)
5. ├─lava::ordinal(x, value, ...)
6. └─lava:::ordinal.lvm(x, value, ...)
7. ├─lava::`addvar<-`(`*tmp*`, value = var)
8. └─lava:::`addvar<-.lvm`(`*tmp*`, value = var)
9. ├─lava::addvar(x, var = value, ...)
10. └─lava:::addvar.lvm(x, var = value, ...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-multigroup.R:31:3'): Missing data analysis ─────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. ├─lava::estimate(m, d, missing = TRUE) at test-multigroup.R:31:3
2. └─lava:::estimate.lvm(m, d, missing = TRUE)
3. └─lava:::estimate.MAR(...)
4. ├─base::subset(Model(x), exogenous(x))
5. └─lava:::subset.lvm(Model(x), exogenous(x))
6. └─lava::lvm(vars)
7. ├─lava::addvar(res, myvar, messages = messages)
8. └─lava:::addvar.lvm(res, myvar, messages = messages)
9. └─lava::reindex(x)
10. └─lava:::mat.lvm(x, res)
11. └─base::cbind(idxM, pidxM)
── Error ('test-multigroup.R:80:5'): Multiple group, constraints ───────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(y[m:v] ~ 1) at test-multigroup.R:80:5
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`intercept<-`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
6. └─lava:::`intercept<-.lvm`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
7. └─lava::reindex(object)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
── Error ('test-sim.R:4:5'): Constrain, transform I ────────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(, ~y + x) at test-sim.R:4:5
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`exogenous<-`(...)
6. └─lava:::`exogenous<-.lvm`(...)
7. └─lava::reindex(x)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
── Error ('test-sim.R:22:5'): Missing ──────────────────────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(y ~ 1) at test-sim.R:22:5
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`intercept<-`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
6. └─lava:::`intercept<-.lvm`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
7. └─lava::reindex(object)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
── Error ('test-sim.R:107:5'): distributions ───────────────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. ├─lava::`distribution<-`(`*tmp*`, ~y, TRUE, value = `<fn>`) at test-sim.R:107:5
2. └─lava:::`distribution<-.lvm`(`*tmp*`, ~y, TRUE, value = `<fn>`)
3. ├─lava::`distribution<-`(`*tmp*`, variable, mdist = TRUE, value = list(gen))
4. └─lava:::`distribution<-.lvm`(...)
5. ├─lava::`addvar<-`(`*tmp*`, value = variable)
6. └─lava:::`addvar<-.lvm`(`*tmp*`, value = variable)
7. ├─lava::addvar(x, var = value, ...)
8. └─lava:::addvar.lvm(x, var = value, ...)
9. └─lava::reindex(x)
10. └─lava:::mat.lvm(x, res)
11. └─base::cbind(idxM, pidxM)
── Error ('test-sim.R:176:5'): eventTime ───────────────────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(y ~ 1) at test-sim.R:176:5
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`intercept<-`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
6. └─lava:::`intercept<-.lvm`(`*tmp*`, ys, value = char2num(xs[intpos[1]]))
7. └─lava::reindex(object)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 173 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 1, NOTE: 6, OK: 6
Version: 1.3.4
Check: examples
Result: ERROR
Running examples in ‘mets-Ex.R’ failed
The error most likely occurred in:
> ### Name: dprint
> ### Title: list, head, print, tail
> ### Aliases: dprint dlist dhead dtail
>
> ### ** Examples
>
> m <- lava::lvm(letters)
Error in cbind(idxM, pidxM) : cannot get data pointer of 'NULL' objects
Calls: <Anonymous> ... addvar -> addvar.lvm -> reindex -> mat.lvm -> cbind
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘basic-dutils.Rmd’ using rmarkdown
--- finished re-building ‘basic-dutils.Rmd’
--- re-building ‘binomial-family.Rmd’ using rmarkdown
--- finished re-building ‘binomial-family.Rmd’
--- re-building ‘binomial-twin.Rmd’ using rmarkdown
--- finished re-building ‘binomial-twin.Rmd’
--- re-building ‘binreg-TRS.rmd’ using rmarkdown
--- finished re-building ‘binreg-TRS.rmd’
--- re-building ‘binreg-ate.Rmd’ using rmarkdown
--- finished re-building ‘binreg-ate.Rmd’
--- re-building ‘binreg.Rmd’ using rmarkdown
--- finished re-building ‘binreg.Rmd’
--- re-building ‘cifreg.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/cifreg_files/figure-html/unnamed-chunk-3-1.png
686x528 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29464 bytes
Input file size = 29578 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24398
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24398
Output IDAT size = 24398 bytes (5066 bytes decrease)
Output file size = 24476 bytes (5102 bytes = 17.25% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/cifreg_files/figure-html/unnamed-chunk-4-1.png
686x528 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17177 bytes
Input file size = 17279 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13514
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13514
Output IDAT size = 13514 bytes (3663 bytes decrease)
Output file size = 13592 bytes (3687 bytes = 21.34% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/cifreg_files/figure-html/unnamed-chunk-5-1.png
686x528 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17762 bytes
Input file size = 17864 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14313
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14313
Output IDAT size = 14313 bytes (3449 bytes decrease)
Output file size = 14391 bytes (3473 bytes = 19.44% decrease)
--- finished re-building ‘cifreg.Rmd’
--- re-building ‘glm-utility.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/glm-utility_files/figure-html/unnamed-chunk-3-1.png
686x528 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26142 bytes
Input file size = 26256 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21135
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21135
Output IDAT size = 21135 bytes (5007 bytes decrease)
Output file size = 21213 bytes (5043 bytes = 19.21% decrease)
--- finished re-building ‘glm-utility.Rmd’
--- re-building ‘haplo-discrete-ttp.Rmd’ using rmarkdown
--- finished re-building ‘haplo-discrete-ttp.Rmd’
--- re-building ‘interval-discrete-survival.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/interval-discrete-survival_files/figure-html/unnamed-chunk-3-1.png
686x528 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5459 bytes
Input file size = 6308 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4417
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4417
Output IDAT size = 4417 bytes (1042 bytes decrease)
Output file size = 4495 bytes (1813 bytes = 28.74% decrease)
--- finished re-building ‘interval-discrete-survival.Rmd’
--- re-building ‘marginal-cox.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/marginal-cox_files/figure-html/unnamed-chunk-5-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9463 bytes
Input file size = 9553 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7088
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7088
Output IDAT size = 7088 bytes (2375 bytes decrease)
Output file size = 7166 bytes (2387 bytes = 24.99% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/marginal-cox_files/figure-html/unnamed-chunk-6-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11738 bytes
Input file size = 11828 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8571
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8571
Output IDAT size = 8571 bytes (3167 bytes decrease)
Output file size = 8649 bytes (3179 bytes = 26.88% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/marginal-cox_files/figure-html/unnamed-chunk-9-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 60671 bytes
Input file size = 60833 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53840
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53840
Output IDAT size = 53840 bytes (6831 bytes decrease)
Output file size = 53918 bytes (6915 bytes = 11.37% decrease)
--- finished re-building ‘marginal-cox.Rmd’
--- re-building ‘mediation-survival.Rmd’ using rmarkdown
--- finished re-building ‘mediation-survival.Rmd’
--- re-building ‘quantitative-twin.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/quantitative-twin_files/figure-html/scatter1-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44960 bytes
Input file size = 45098 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36549
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36549
Output IDAT size = 36549 bytes (8411 bytes decrease)
Output file size = 36627 bytes (8471 bytes = 18.78% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/quantitative-twin_files/figure-html/scatter2-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 52082 bytes
Input file size = 52232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 40802
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 40802
Output IDAT size = 40802 bytes (11280 bytes decrease)
Output file size = 40880 bytes (11352 bytes = 21.73% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/quantitative-twin_files/figure-html/marg1-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 10242 bytes
Input file size = 10332 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7520
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7520
Output IDAT size = 7520 bytes (2722 bytes decrease)
Output file size = 7598 bytes (2734 bytes = 26.46% decrease)
Quitting from lines 244-246 [lmeqmarg] (quantitative-twin.Rmd)
Error: processing vignette 'quantitative-twin.Rmd' failed with diagnostics:
cannot get data pointer of 'NULL' objects
--- failed re-building ‘quantitative-twin.Rmd’
--- re-building ‘recurrent-events.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-4-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14723 bytes
Input file size = 14813 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11911
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11911
Output IDAT size = 11911 bytes (2812 bytes decrease)
Output file size = 11989 bytes (2824 bytes = 19.06% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-6-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18946 bytes
Input file size = 19048 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15389
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15389
Output IDAT size = 15389 bytes (3557 bytes decrease)
Output file size = 15467 bytes (3581 bytes = 18.80% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-7-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15434 bytes
Input file size = 15524 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12690
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12690
Output IDAT size = 12690 bytes (2744 bytes decrease)
Output file size = 12768 bytes (2756 bytes = 17.75% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-8-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9176 bytes
Input file size = 9266 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7268
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7268
Output IDAT size = 7268 bytes (1908 bytes decrease)
Output file size = 7346 bytes (1920 bytes = 20.72% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-10-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11918 bytes
Input file size = 12008 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9348
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9348
Output IDAT size = 9348 bytes (2570 bytes decrease)
Output file size = 9426 bytes (2582 bytes = 21.50% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-13-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11843 bytes
Input file size = 11933 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9192
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9192
Output IDAT size = 9192 bytes (2651 bytes decrease)
Output file size = 9270 bytes (2663 bytes = 22.32% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-18-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11266 bytes
Input file size = 11356 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9090
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9090
Output IDAT size = 9090 bytes (2176 bytes decrease)
Output file size = 9168 bytes (2188 bytes = 19.27% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-19-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14034 bytes
Input file size = 14124 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9564
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9564
Output IDAT size = 9564 bytes (4470 bytes decrease)
Output file size = 9642 bytes (4482 bytes = 31.73% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-20-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8398 bytes
Input file size = 8488 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6705
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6705
Output IDAT size = 6705 bytes (1693 bytes decrease)
Output file size = 6783 bytes (1705 bytes = 20.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-21-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26681 bytes
Input file size = 26795 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18920
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18920
Output IDAT size = 18920 bytes (7761 bytes decrease)
Output file size = 18998 bytes (7797 bytes = 29.10% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-22-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19224 bytes
Input file size = 19326 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15449
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15449
Output IDAT size = 15449 bytes (3775 bytes decrease)
Output file size = 15527 bytes (3799 bytes = 19.66% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-24-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 12167 bytes
Input file size = 12257 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9086
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9086
Output IDAT size = 9086 bytes (3081 bytes decrease)
Output file size = 9164 bytes (3093 bytes = 25.23% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/recurrent-events_files/figure-html/unnamed-chunk-25-1.png
350x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19643 bytes
Input file size = 19745 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16222
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16222
Output IDAT size = 16222 bytes (3421 bytes decrease)
Output file size = 16300 bytes (3445 bytes = 17.45% decrease)
--- finished re-building ‘recurrent-events.Rmd’
--- re-building ‘rmst-ate.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/rmst-ate_files/figure-html/unnamed-chunk-2-1.png
686x528 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 54326 bytes
Input file size = 54476 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46859
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46859
Output IDAT size = 46859 bytes (7467 bytes decrease)
Output file size = 46937 bytes (7539 bytes = 13.84% decrease)
--- finished re-building ‘rmst-ate.Rmd’
--- re-building ‘survival-ate.Rmd’ using rmarkdown
--- finished re-building ‘survival-ate.Rmd’
--- re-building ‘time-to-event-family-studies-arev.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/survival-marginal-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13904 bytes
Input file size = 13994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10347
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10347
Output IDAT size = 10347 bytes (3557 bytes decrease)
Output file size = 10425 bytes (3569 bytes = 25.50% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/concordance-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14734 bytes
Input file size = 14824 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11206
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11206
Output IDAT size = 11206 bytes (3528 bytes decrease)
Output file size = 11284 bytes (3540 bytes = 23.88% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/unnamed-chunk-9-1.png
357x275 pixels, 8 bits/pixel, 251 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5486 bytes
Input file size = 6329 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4901
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4901
Output IDAT size = 4901 bytes (585 bytes decrease)
Output file size = 4979 bytes (1350 bytes = 21.33% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/concordance2-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16105 bytes
Input file size = 16195 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12219
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12219
Output IDAT size = 12219 bytes (3886 bytes decrease)
Output file size = 12297 bytes (3898 bytes = 24.07% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/concordance3-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17119 bytes
Input file size = 17221 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13192
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13192
Output IDAT size = 13192 bytes (3927 bytes decrease)
Output file size = 13270 bytes (3951 bytes = 22.94% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/unnamed-chunk-17-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8824 bytes
Input file size = 8914 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6843
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6843
Output IDAT size = 6843 bytes (1981 bytes decrease)
Output file size = 6921 bytes (1993 bytes = 22.36% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/biprobittime1-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 12320 bytes
Input file size = 12410 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9605
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9605
Output IDAT size = 9605 bytes (2715 bytes decrease)
Output file size = 9683 bytes (2727 bytes = 21.97% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/unnamed-chunk-19-1.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8465 bytes
Input file size = 8555 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6375
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6375
Output IDAT size = 6375 bytes (2090 bytes decrease)
Output file size = 6453 bytes (2102 bytes = 24.57% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/unnamed-chunk-19-2.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8803 bytes
Input file size = 8893 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6785
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6785
Output IDAT size = 6785 bytes (2018 bytes decrease)
Output file size = 6863 bytes (2030 bytes = 22.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/unnamed-chunk-19-3.png
357x275 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8617 bytes
Input file size = 8707 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6387
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6387
Output IDAT size = 6387 bytes (2230 bytes decrease)
Output file size = 6465 bytes (2242 bytes = 25.75% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/vign_test/mets/vignettes/time-to-event-family-studies-arev_files/figure-html/unnamed-chunk-19-4.png
357x275 pixels, 8 bits/pixel, 213 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 2376 bytes
Input file size = 3105 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1985
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1985
Output IDAT size = 1985 bytes (391 bytes decrease)
Output file size = 2063 bytes (1042 bytes = 33.56% decrease)
--- finished re-building ‘time-to-event-family-studies-arev.Rmd’
--- re-building ‘twostage-survival.Rmd’ using rmarkdown
--- finished re-building ‘twostage-survival.Rmd’
SUMMARY: processing the following file failed:
‘quantitative-twin.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.3.4
Check: installed package size
Result: NOTE
installed size is 27.3Mb
sub-directories of 1Mb or more:
R 2.0Mb
doc 2.8Mb
libs 20.6Mb
Flavors: 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
Current CRAN status: ERROR: 1, NOTE: 4, OK: 8
Version: 0.5
Check: examples
Result: ERROR
Running examples in ‘targeted-Ex.R’ failed
The error most likely occurred in:
> ### Name: alean
> ### Title: Assumption Lean inference for generalized linear model
> ### parameters
> ### Aliases: alean
>
> ### ** Examples
>
>
> sim1 <- function(n, family=gaussian(), ...) {
+ m <- lvm() |>
+ distribution(~ y, binomial.lvm()) |>
+ regression('a', value=function(l) l) |>
+ regression('y', value=function(a,l) a + l)
+ if (family$family=="binomial")
+ distribution(m, ~a) <- binomial.lvm()
+ sim(m, n)
+ }
>
> library(splines)
> f <- binomial()
> d <- sim1(1e4, family=f)
Error in cbind(idxM, pidxM) : cannot get data pointer of 'NULL' objects
Calls: sim1 ... exogenous<- -> exogenous<-.lvm -> reindex -> mat.lvm -> cbind
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.5
Check: tests
Result: ERROR
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> suppressPackageStartupMessages(library("testthat"))
> test_check("targeted")
Loading required package: targeted
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 15 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-riskreg.R:4:1'): (code run outside of `test_that()`) ───────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─lava::lvm(...) at test-riskreg.R:4:1
2. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
3. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
4. └─lava::procformula(object, value, ...)
5. ├─lava::`intercept<-`(...)
6. └─lava:::`intercept<-.lvm`(...)
7. └─lava::reindex(object)
8. └─lava:::mat.lvm(x, res)
9. └─base::cbind(idxM, pidxM)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 15 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.5
Check: installed package size
Result: NOTE
installed size is 15.0Mb
sub-directories of 1Mb or more:
doc 1.1Mb
libs 13.3Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.