* using log directory ‘/data/localhost/ripley/R/packages/tests-noLD/freesurferformats.Rcheck’ * using R Under development (unstable) (2026-09-25 r90589) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-09-25 03:12:13 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘freesurferformats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘freesurferformats’ version ‘1.1.0’ * 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 ‘freesurferformats’ can be installed ... [14s/15s] 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... 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 ... [33s/34s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [14s/15s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [73s/76s] [73s/76s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(freesurferformats) > > test_check("freesurferformats") CIFTI-2 file '/data/localhost/ripley/R/packages/tests-noLD/freesurferformats.Rcheck/freesurferformats/extdata/cifti/tiny.pconn.nii' (NIFTI-2, 4 data values per matrix entry). Matrix dimensions: 3 x 3 (CIFTI dimension 0, 1). Dimension 0,1: parcels, 3,3 per dimension. 3 parcels, first: PARCEL_A, PARCEL_B, PARCEL_C Connectome matrix: 3 x 3 values of type 'double'. Parcels (matrix dimension 0): 3, first ones: PARCEL_A, PARCEL_B, PARCEL_C [1] "Label table cdata (region names for the rows below):" [1] "unknown" "bankssts" [3] "caudalanteriorcingulate" "caudalmiddlefrontal" [5] "corpuscallosum" "cuneus" [7] "entorhinal" "fusiform" [9] "inferiorparietal" "inferiortemporal" [11] "isthmuscingulate" "lateraloccipital" [13] "lateralorbitofrontal" "lingual" [15] "medialorbitofrontal" "middletemporal" [17] "parahippocampal" "paracentral" [19] "parsopercularis" "parsorbitalis" [21] "parstriangularis" "pericalcarine" [23] "postcentral" "posteriorcingulate" [25] "precentral" "precuneus" [27] "rostralanteriorcingulate" "rostralmiddlefrontal" [29] "superiorfrontal" "superiorparietal" [31] "superiortemporal" "supramarginal" [33] "frontalpole" "temporalpole" [35] "transversetemporal" "insula" [1] "Label table attribute columns:" Red Green Blue Alpha Key Index unknown 25 5 25 0 1639705 1639705 bankssts 25 100 40 0 2647065 2647065 caudalanteriorcingulate 125 100 160 0 10511485 10511485 caudalmiddlefrontal 100 25 0 0 6500 6500 corpuscallosum 120 70 50 0 3294840 3294840 cuneus 220 20 100 0 6558940 6558940 entorhinal 220 20 10 0 660700 660700 fusiform 180 220 140 0 9231540 9231540 inferiorparietal 220 60 220 0 14433500 14433500 inferiortemporal 180 40 120 0 7874740 7874740 isthmuscingulate 140 20 140 0 9180300 9180300 lateraloccipital 20 30 140 0 9182740 9182740 lateralorbitofrontal 35 75 50 0 3296035 3296035 lingual 225 140 140 0 9211105 9211105 medialorbitofrontal 200 35 75 0 4924360 4924360 middletemporal 160 100 50 0 3302560 3302560 parahippocampal 20 220 60 0 3988500 3988500 paracentral 60 220 60 0 3988540 3988540 parsopercularis 220 180 140 0 9221340 9221340 parsorbitalis 20 100 50 0 3302420 3302420 parstriangularis 220 60 20 0 1326300 1326300 pericalcarine 120 100 60 0 3957880 3957880 postcentral 220 20 20 0 1316060 1316060 posteriorcingulate 220 180 220 0 14464220 14464220 precentral 60 20 220 0 14423100 14423100 precuneus 160 140 180 0 11832480 11832480 rostralanteriorcingulate 80 20 140 0 9180240 9180240 rostralmiddlefrontal 75 50 125 0 8204875 8204875 superiorfrontal 20 220 160 0 10542100 10542100 superiorparietal 20 180 140 0 9221140 9221140 superiortemporal 140 220 220 0 14474380 14474380 supramarginal 80 160 20 0 1351760 1351760 frontalpole 100 0 100 0 6553700 6553700 temporalpole 70 20 170 0 11146310 11146310 transversetemporal 150 150 200 0 13145750 13145750 insula 255 192 32 0 2146559 2146559 Saving _problems/test-write_fs_transform-182.R Saving _problems/test-write_fs_transform-182.R Saving _problems/test-write_fs_transform-182.R Saving _problems/test-write_fs_transform-182.R [ FAIL 4 | WARN 0 | SKIP 48 | PASS 3467 ] ══ Skipped tests (48) ══════════════════════════════════════════════════════════ • Freesurfer installation with GCA file available. (1): 'test-read_fs_annot.R:173:3' • On CRAN (29): 'test-cifti-connectome-official.R:16:3', 'test-cifti-connectome-official.R:51:3', 'test-cifti-connectome-official.R:77:3', 'test-cifti-connectome-official.R:94:3', 'test-cifti.R:5:3', 'test-cifti2.R:16:3', 'test-cifti2.R:49:3', 'test-cifti2.R:77:3', 'test-cifti2.R:121:3', 'test-gifti_xml_tools.R:2:3', 'test-read_dti_tcktsf.R:280:3', 'test-read_fs_annot.R:78:3', 'test-read_fs_patch.R:3:3', 'test-read_fs_patch.R:25:3', 'test-read_fs_surface.R:2:3', 'test-read_fs_surface.R:34:3', 'test-read_fs_surface.R:58:3', 'test-read_nifti1.R:2:3', 'test-read_nifti1.R:21:3', 'test-read_nifti1.R:39:3', 'test-read_nifti1.R:57:3', 'test-read_nifti1.R:77:3', 'test-read_nifti2.R:2:3', 'test-read_nifti2.R:26:3', 'test-read_nifti2.R:42:3', 'test-surface_dist.R:2:3', 'test-write_cifti.R:386:3', 'test-write_fs_annot.R:122:3', 'test-write_fs_surface.R:38:3' • Test data missing. (12): 'test-itk_transform.R:115:3', 'test-mgh2nii.R:101:5', 'test-read_analyze.R:297:5', 'test-read_dti_trk.R:231:3', 'test-read_fs_surface.R:85:3', 'test-read_nifti2_extensions.R:100:3', 'test-read_nrrd.R:135:5', 'test-read_nrrd.R:148:5', 'test-read_nrrd.R:231:5', 'test-read_nrrd.R:247:5', 'test-read_nrrd.R:261:5', 'test-vtk.R:379:3' • extra_test_data not available (1): 'test-read_cifti_header.R:302:3' • extra_test_data not available in this environment (a git checkout of the repository is required). (5): 'test-mgh_nii_crossfile.R:16:3', 'test-mgh_nii_crossfile.R:54:3', 'test-mgh_nii_crossfile.R:83:3', 'test-nifti_read_order.R:112:3', 'test-read_dwi_gradients.R:243:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-write_fs_transform.R:182:5'): Written matrices are read back exactly. ── Expected `read.fs.transform(out_file)$matrix` to be identical to `rotation`. Differences: Objects equal but not identical ── Failure ('test-write_fs_transform.R:182:5'): Written matrices are read back exactly. ── Expected `read.fs.transform(out_file)$matrix` to be identical to `rotation`. Differences: Objects equal but not identical ── Failure ('test-write_fs_transform.R:182:5'): Written matrices are read back exactly. ── Expected `read.fs.transform(out_file)$matrix` to be identical to `rotation`. Differences: Objects equal but not identical ── Failure ('test-write_fs_transform.R:182:5'): Written matrices are read back exactly. ── Expected `read.fs.transform(out_file)$matrix` to be identical to `rotation`. Differences: Objects equal but not identical [ FAIL 4 | WARN 0 | SKIP 48 | PASS 3467 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s/14s] OK * checking PDF version of manual ... [22s/24s] OK * checking HTML version of manual ... [13s/13s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-noLD/freesurferformats.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:47.03, 201.10 + 14.03