Check results for 'ComBatFamQC'

using R version 4.3.3 (2024-02-29)
using platform: aarch64-apple-darwin20 (64-bit)
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.4
using session charset: UTF-8
checking for file ‘ComBatFamQC/DESCRIPTION’ ... OK
this is package ‘ComBatFamQC’ version ‘1.0.5’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘ComBatFamQC’ can be installed ... [6s/6s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [1s/1s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [5s/6s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [0s/0s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [8s/8s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [70s/75s] ERROR Running ‘testthat.R’ [70s/75s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(ComBatFamQC) > > test_check("ComBatFamQC") Loading required package: shiny GAMLSS-RS iteration 1: Global Deviance = 11577.26 GAMLSS-RS iteration 2: Global Deviance = 11577.26 GAMLSS-RS iteration 3: Global Deviance = 11577.26 GAMLSS-RS iteration 1: Global Deviance = 11582.7 GAMLSS-RS iteration 2: Global Deviance = 11582.68 GAMLSS-RS iteration 3: Global Deviance = 11582.68 [1] "Batch levels that contain less than 3 observations are dropped: no batch level is dropped." [1] "A noticeable deviation of the mean from zero in the additive-residual box plot indicates the presence of an additive batch effect" [1] "A substantial variation in the multiplicative-residual box plot demonstrates a potential multiplicative batch effect." [1] "eg: covariate1*covariate2,covariate3*covariate4 " Starting data preparation for the batch effect diagnostic and harmonization stage... Taking the result from the visual preparation stage as input... No observation is dropped due to missing values. Starting Empirical Bayes assumption check... Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting Empirical Bayes assumption check... Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... Starting data preparation for the batch effect diagnostic and harmonization stage... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... Starting data preparation for the batch effect diagnostic and harmonization stage... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... Starting data preparation for the batch effect diagnostic and harmonization stage... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting out-of-sample harmonization using the saved ComBat Model... Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: 1 level(s) are dropped, corresponding to 2 observations. Starting out-of-sample harmonization using the reference dataset... Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` The reference data is included in the new unharmonized dataset Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: 1 level(s) are dropped, corresponding to 2 observations. Starting out-of-sample harmonization using the reference dataset... Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` The reference data is included in the new unharmonized dataset Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... Taking the result from the visual preparation stage as input... No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No observation is dropped due to missing values. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. New names: * `residual_y` -> `residual_y...1` * `residual_y` -> `residual_y...2` * `residual_y` -> `residual_y...3` * `residual_y` -> `residual_y...4` Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. New names: * `X3` -> `X3...1` * `X3` -> `X3...2` * `X3` -> `X3...3` * `X3` -> `X3...4` Starting data preparation for the post-harmonization stage... No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. New names: * `residual_y` -> `residual_y...1` * `residual_y` -> `residual_y...2` * `residual_y` -> `residual_y...3` * `residual_y` -> `residual_y...4` Starting data preparation for the post-harmonization stage... No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No observation is dropped due to missing values. New names: * `residual_y` -> `residual_y...1` * `residual_y` -> `residual_y...2` * `residual_y` -> `residual_y...3` * `residual_y` -> `residual_y...4` Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. New names: * `residual_y` -> `residual_y...1` * `residual_y` -> `residual_y...2` * `residual_y` -> `residual_y...3` * `residual_y` -> `residual_y...4` Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Statistic Numer.DF Pseudo.R2 Analytic.p.value (Omnibus) 0.0495 2 0.0472 < 1e-20 *** manufacs 0.0495 2 0.0472 < 1e-20 *** --- Signif. codes: 0 "***" 0.001 "**" 0.01 "*" 0.05 "." 0.1 " " 1Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Statistic Numer.DF Pseudo.R2 Analytic.p.value (Omnibus) 0.363 2 0.266 < 1e-20 *** manufacs 0.363 2 0.266 < 1e-20 *** --- Signif. codes: 0 "***" 0.001 "**" 0.01 "*" 0.05 "." 0.1 " " 1refitting model(s) with ML (instead of REML) refitting model(s) with ML (instead of REML) refitting model(s) with ML (instead of REML) refitting model(s) with ML (instead of REML) Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Statistic Numer.DF Pseudo.R2 Analytic.p.value (Omnibus) 0.0534 2 0.0507 < 1e-20 *** manufacs 0.0534 2 0.0507 < 1e-20 *** --- Signif. codes: 0 "***" 0.001 "**" 0.01 "*" 0.05 "." 0.1 " " 1[ FAIL 1 | WARN 101 | SKIP 0 | PASS 232 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-comfam_shiny.R:49:5'): comfam_shiny server logic works correctly ── <packageNotFoundError/error/condition> Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'systemfonts' Backtrace: ▆ 1. ├─shiny::testServer(...) at test-comfam_shiny.R:4:3 2. │ ├─shiny:::withMockContext(...) 3. │ │ ├─shiny::isolate(...) 4. │ │ │ ├─shiny::..stacktraceoff..(...) 5. │ │ │ └─ctx$run(...) 6. │ │ │ ├─promises::with_promise_domain(...) 7. │ │ │ │ └─domain$wrapSync(expr) 8. │ │ │ ├─shiny::withReactiveDomain(...) 9. │ │ │ │ └─promises::with_promise_domain(...) 10. │ │ │ │ └─domain$wrapSync(expr) 11. │ │ │ │ └─base::force(expr) 12. │ │ │ ├─shiny::captureStackTraces(...) 13. │ │ │ │ └─promises::with_promise_domain(...) 14. │ │ │ │ └─domain$wrapSync(expr) 15. │ │ │ │ └─base::withCallingHandlers(expr, error = doCaptureStack) 16. │ │ │ └─env$runWith(self, func) 17. │ │ │ └─shiny (local) contextFunc() 18. │ │ │ └─shiny::..stacktraceon..(expr) 19. │ │ ├─shiny::withReactiveDomain(...) 20. │ │ │ └─promises::with_promise_domain(...) 21. │ │ │ └─domain$wrapSync(expr) 22. │ │ │ └─base::force(expr) 23. │ │ └─withr::with_options(...) 24. │ │ └─base::force(code) 25. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env()) 26. ├─testthat::expect_true(!is.null(output$pca)) at test-comfam_shiny.R:49:5 27. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 28. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 29. ├─output$pca 30. ├─shiny:::`$.shinyoutput`(output, pca) 31. │ └─.subset2(x, "impl")$getOutput(name) 32. │ └─base::stop(v$err) 33. └─shiny (local) `<fn>`(`<pckgNtFE>`) [ FAIL 1 | WARN 101 | SKIP 0 | PASS 232 ] Error: Test failures Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking re-building of vignette outputs ... [9s/9s] OK
checking PDF version of manual ... [4s/4s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '