Last updated on 2019-06-12 09:50:12 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.6 | 10.47 | 157.22 | 167.69 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.6 | 8.34 | 121.76 | 130.10 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.6 | 205.97 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.6 | 199.79 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.0.6 | 27.00 | 312.00 | 339.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.6 | 11.63 | 151.81 | 163.44 | ERROR | |
| r-patched-solaris-x86 | 1.0.6 | 312.10 | NOTE | |||
| r-release-linux-x86_64 | 1.0.6 | 11.15 | 151.69 | 162.84 | ERROR | |
| r-release-windows-ix86+x86_64 | 1.0.6 | 41.00 | 303.00 | 344.00 | OK | |
| r-release-osx-x86_64 | 1.0.6 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.6 | 18.00 | 976.00 | 994.00 | ERROR | |
| r-oldrel-osx-x86_64 | 1.0.6 | NOTE |
Version: 1.0.6
Check: tests
Result: ERROR
Running 'testthat.R' [1m/13m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(radtools)
>
> test_check("radtools")
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-ort.gz'
Content type 'application/gzip' length 246877 bytes (241 KB)
==================================================
downloaded 241 KB
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-brain.gz'
Content type 'application/gzip' length 261311 bytes (255 KB)
==================================================
downloaded 255 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-head.gz'
Content type 'application/gzip' length 70273 bytes (68 KB)
==================================================
downloaded 68 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-knee.gz'
Content type 'application/gzip' length 69484 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-8-16x-heart.gz'
Content type 'application/gzip' length 337207 bytes (329 KB)
==================================================
downloaded 329 KB
trying URL 'http://barre.nom.fr/medical/samples/files/NM-MONO2-16-13x-heart.gz'
Content type 'application/gzip' length 24002 bytes (23 KB)
==================================================
downloaded 23 KB
trying URL 'http://barre.nom.fr/medical/samples/files/US-MONO2-8-8x-execho.gz'
Content type 'application/gzip' length 86068 bytes (84 KB)
==================================================
downloaded 84 KB
trying URL 'http://www.dclunie.com/images/charset/charsettests.20070405.tar.bz2'
Content type 'binary/octet-stream' length 6110 bytes
==================================================
downloaded 6110 bytes
trying URL 'http://www.dclunie.com/images/compressed/deflate_tests_release.tar.gz'
Content type 'application/x-gzip' length 65476 bytes (63 KB)
==================================================
downloaded 63 KB
trying URL 'http://www.dclunie.com/images/signedrange/signedrangeimages.tar.bz2'
Content type 'application/x-bzip2' length 278192 bytes (271 KB)
==================================================
downloaded 271 KB
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "/tmp/RtmpGfMAZV/minimal"
Could not read NIfTI-1 object from path /tmp/RtmpGfMAZV/minimal
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "/tmp/RtmpGfMAZV/newsirp_final_XML.nii"
Could not read NIfTI-1 object from path /tmp/RtmpGfMAZV/newsirp_final_XML.nii
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'http://www.neuromorphometrics.com/1103_3.tgz'
Content type 'application/x-tar' length 7286064 bytes (6.9 MB)
==================================================
downloaded 6.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR.nii.gz'
Content type 'application/octet-stream' length 1351404 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR_regToT1.nii.gz'
Content type 'application/octet-stream' length 13690259 bytes (13.1 MB)
==================================================
downloaded 13.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI.nii.gz'
Content type 'application/octet-stream' length 5279 bytes
==================================================
downloaded 5279 bytes
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI_regToT1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 302833 bytes (295 KB)
==================================================
downloaded 295 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1.nii.gz'
Content type 'application/octet-stream' length 3763118 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 6603933 bytes (6.3 MB)
==================================================
downloaded 6.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_brain.nii.gz'
Content type 'application/octet-stream' length 3086068 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_mask.nii.gz'
Content type 'application/octet-stream' length 68732 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/MNI152_T1_1mm_brain.nii.gz'
Content type 'application/octet-stream' length 3219212 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE.nii.gz'
Content type 'application/octet-stream' length 7744679 bytes (7.4 MB)
==================================================
downloaded 7.4 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE_mask.nii.gz'
Content type 'application/octet-stream' length 58905 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/FLIRT_113-01-T2w_regToT1.nii.gz'
Content type 'application/octet-stream' length 29975529 bytes (28.6 MB)
==================================================
downloaded 28.6 MB
-- 1. Error: NIfTI import (@test_image_import_nifti.R#7) ----------------------
no applicable method for 'img_data_to_3D_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_filtered_func, expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func,
coord_extra_dim = 180)), c(64, 64, 21))) at testthat/test_image_import_nifti.R:7
2: expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)),
c(64, 64, 21)) at /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)
-- 2. Error: NIfTI metadata (@test_metadata_nifti.R#6) ------------------------
no applicable method for 'num_slices' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, expect_equal(num_slices(nifti_data_avg152T1_LR),
91)) at testthat/test_metadata_nifti.R:6
2: expect_equal(num_slices(nifti_data_avg152T1_LR), 91) at /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: num_slices(nifti_data_avg152T1_LR)
-- 3. Error: View slice - for CRAN (@test_view.R#15) --------------------------
no applicable method for 'img_data_to_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR),
10)) at testthat/test_view.R:15
2: view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR), 10) at /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: img_data_to_mat(nifti_data_avg152T1_LR)
== testthat results ===========================================================
OK: 127 SKIPPED: 3 WARNINGS: 15 FAILED: 3
1. Error: NIfTI import (@test_image_import_nifti.R#7)
2. Error: NIfTI metadata (@test_metadata_nifti.R#6)
3. Error: View slice - for CRAN (@test_view.R#15)
Error: testthat unit tests failed
In addition: Warning messages:
1: In dir.create(outdir_nifti, recursive = TRUE) :
'/tmp/RtmpGfMAZV' already exists
2: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz': HTTP status was '502 Bad Gateway'
3: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz': HTTP status was '502 Bad Gateway'
4: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz': HTTP status was '502 Bad Gateway'
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [1m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(radtools)
>
> test_check("radtools")
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-ort.gz'
Content type 'application/gzip' length 246877 bytes (241 KB)
==================================================
downloaded 241 KB
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-brain.gz'
Content type 'application/gzip' length 261311 bytes (255 KB)
==================================================
downloaded 255 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-head.gz'
Content type 'application/gzip' length 70273 bytes (68 KB)
==================================================
downloaded 68 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-knee.gz'
Content type 'application/gzip' length 69484 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-8-16x-heart.gz'
Content type 'application/gzip' length 337207 bytes (329 KB)
==================================================
downloaded 329 KB
trying URL 'http://barre.nom.fr/medical/samples/files/NM-MONO2-16-13x-heart.gz'
Content type 'application/gzip' length 24002 bytes (23 KB)
==================================================
downloaded 23 KB
trying URL 'http://barre.nom.fr/medical/samples/files/US-MONO2-8-8x-execho.gz'
Content type 'application/gzip' length 86068 bytes (84 KB)
==================================================
downloaded 84 KB
trying URL 'http://www.dclunie.com/images/charset/charsettests.20070405.tar.bz2'
Content type 'binary/octet-stream' length 6110 bytes
==================================================
downloaded 6110 bytes
trying URL 'http://www.dclunie.com/images/compressed/deflate_tests_release.tar.gz'
Content type 'application/x-gzip' length 65476 bytes (63 KB)
==================================================
downloaded 63 KB
trying URL 'http://www.dclunie.com/images/signedrange/signedrangeimages.tar.bz2'
Content type 'application/x-bzip2' length 278192 bytes (271 KB)
==================================================
downloaded 271 KB
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "/home/hornik/tmp/scratch/RtmpHgbaTd/minimal"
Could not read NIfTI-1 object from path /home/hornik/tmp/scratch/RtmpHgbaTd/minimal
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "/home/hornik/tmp/scratch/RtmpHgbaTd/newsirp_final_XML.nii"
Could not read NIfTI-1 object from path /home/hornik/tmp/scratch/RtmpHgbaTd/newsirp_final_XML.nii
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'http://www.neuromorphometrics.com/1103_3.tgz'
Content type 'application/x-tar' length 7286064 bytes (6.9 MB)
==================================================
downloaded 6.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR.nii.gz'
Content type 'application/octet-stream' length 1351404 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR_regToT1.nii.gz'
Content type 'application/octet-stream' length 13690259 bytes (13.1 MB)
==================================================
downloaded 13.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI.nii.gz'
Content type 'application/octet-stream' length 5279 bytes
==================================================
downloaded 5279 bytes
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI_regToT1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 302833 bytes (295 KB)
==================================================
downloaded 295 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1.nii.gz'
Content type 'application/octet-stream' length 3763118 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 6603933 bytes (6.3 MB)
==================================================
downloaded 6.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_brain.nii.gz'
Content type 'application/octet-stream' length 3086068 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_mask.nii.gz'
Content type 'application/octet-stream' length 68732 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/MNI152_T1_1mm_brain.nii.gz'
Content type 'application/octet-stream' length 3219212 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE.nii.gz'
Content type 'application/octet-stream' length 7744679 bytes (7.4 MB)
==================================================
downloaded 7.4 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE_mask.nii.gz'
Content type 'application/octet-stream' length 58905 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/FLIRT_113-01-T2w_regToT1.nii.gz'
Content type 'application/octet-stream' length 29975529 bytes (28.6 MB)
==================================================
downloaded 28.6 MB
── 1. Error: NIfTI import (@test_image_import_nifti.R#7) ──────────────────────
no applicable method for 'img_data_to_3D_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_filtered_func, expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func,
coord_extra_dim = 180)), c(64, 64, 21))) at testthat/test_image_import_nifti.R:7
2: expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)),
c(64, 64, 21)) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)
── 2. Error: NIfTI metadata (@test_metadata_nifti.R#6) ────────────────────────
no applicable method for 'num_slices' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, expect_equal(num_slices(nifti_data_avg152T1_LR),
91)) at testthat/test_metadata_nifti.R:6
2: expect_equal(num_slices(nifti_data_avg152T1_LR), 91) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: num_slices(nifti_data_avg152T1_LR)
── 3. Error: View slice - for CRAN (@test_view.R#15) ──────────────────────────
no applicable method for 'img_data_to_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR),
10)) at testthat/test_view.R:15
2: view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR), 10) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: img_data_to_mat(nifti_data_avg152T1_LR)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 127 SKIPPED: 3 WARNINGS: 15 FAILED: 3
1. Error: NIfTI import (@test_image_import_nifti.R#7)
2. Error: NIfTI metadata (@test_metadata_nifti.R#6)
3. Error: View slice - for CRAN (@test_view.R#15)
Error: testthat unit tests failed
In addition: Warning messages:
1: In dir.create(outdir_nifti, recursive = TRUE) :
'/home/hornik/tmp/scratch/RtmpHgbaTd' already exists
2: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz': HTTP status was '502 Bad Gateway'
3: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz': HTTP status was '502 Bad Gateway'
4: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz': HTTP status was '502 Bad Gateway'
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.6
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘R.utils’ ‘TCIApathfinder’ ‘xfun’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 1.0.6
Check: tests
Result: ERROR
Running 'testthat.R' [13m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(radtools)
>
> test_check("radtools")
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-ort.gz'
Content type 'application/x-gzip' length 246877 bytes (241 KB)
==================================================
downloaded 241 KB
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-brain.gz'
Content type 'application/x-gzip' length 261311 bytes (255 KB)
==================================================
downloaded 255 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-head.gz'
Content type 'application/x-gzip' length 70273 bytes (68 KB)
==================================================
downloaded 68 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-knee.gz'
Content type 'application/x-gzip' length 69484 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-8-16x-heart.gz'
Content type 'application/x-gzip' length 337207 bytes (329 KB)
==================================================
downloaded 329 KB
trying URL 'http://barre.nom.fr/medical/samples/files/NM-MONO2-16-13x-heart.gz'
Content type 'application/x-gzip' length 24002 bytes (23 KB)
==================================================
downloaded 23 KB
trying URL 'http://barre.nom.fr/medical/samples/files/US-MONO2-8-8x-execho.gz'
Content type 'application/x-gzip' length 86068 bytes (84 KB)
==================================================
downloaded 84 KB
trying URL 'http://www.dclunie.com/images/charset/charsettests.20070405.tar.bz2'
Content type 'binary/octet-stream' length 6110 bytes
==================================================
downloaded 6110 bytes
trying URL 'http://www.dclunie.com/images/compressed/deflate_tests_release.tar.gz'
Content type 'application/x-gzip' length 65476 bytes (63 KB)
==================================================
downloaded 63 KB
trying URL 'http://www.dclunie.com/images/signedrange/signedrangeimages.tar.bz2'
Content type 'application/x-bzip2' length 278192 bytes (271 KB)
==================================================
downloaded 271 KB
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "D:/temp/RtmpWcgO7c/minimal"
Could not read NIfTI-1 object from path D:/temp/RtmpWcgO7c/minimal
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "D:/temp/RtmpWcgO7c/newsirp_final_XML.nii"
Could not read NIfTI-1 object from path D:/temp/RtmpWcgO7c/newsirp_final_XML.nii
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'http://www.neuromorphometrics.com/1103_3.tgz'
Content type 'application/x-tar' length 7286064 bytes (6.9 MB)
==================================================
downloaded 6.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR.nii.gz'
Content type 'application/octet-stream' length 1351404 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR_regToT1.nii.gz'
Content type 'application/octet-stream' length 13690259 bytes (13.1 MB)
==================================================
downloaded 13.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI.nii.gz'
Content type 'application/octet-stream' length 5279 bytes
==================================================
downloaded 5279 bytes
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI_regToT1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 302833 bytes (295 KB)
==================================================
downloaded 295 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1.nii.gz'
Content type 'application/octet-stream' length 3763118 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 6603933 bytes (6.3 MB)
==================================================
downloaded 6.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_brain.nii.gz'
Content type 'application/octet-stream' length 3086068 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_mask.nii.gz'
Content type 'application/octet-stream' length 68732 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/MNI152_T1_1mm_brain.nii.gz'
Content type 'application/octet-stream' length 3219212 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE.nii.gz'
Content type 'application/octet-stream' length 7744679 bytes (7.4 MB)
==================================================
downloaded 7.4 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE_mask.nii.gz'
Content type 'application/octet-stream' length 58905 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/FLIRT_113-01-T2w_regToT1.nii.gz'
Content type 'application/octet-stream' length 29975529 bytes (28.6 MB)
==================================================
downloaded 28.6 MB
-- 1. Error: NIfTI import (@test_image_import_nifti.R#7) ----------------------
no applicable method for 'img_data_to_3D_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_filtered_func, expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func,
coord_extra_dim = 180)), c(64, 64, 21))) at testthat/test_image_import_nifti.R:7
2: expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)),
c(64, 64, 21)) at d:\RCompile\CRANpkg\local\3.7\radtools.Rcheck\tests\testthat\helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)
-- 2. Error: NIfTI metadata (@test_metadata_nifti.R#6) ------------------------
no applicable method for 'num_slices' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, expect_equal(num_slices(nifti_data_avg152T1_LR),
91)) at testthat/test_metadata_nifti.R:6
2: expect_equal(num_slices(nifti_data_avg152T1_LR), 91) at d:\RCompile\CRANpkg\local\3.7\radtools.Rcheck\tests\testthat\helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: num_slices(nifti_data_avg152T1_LR)
-- 3. Error: View slice - for CRAN (@test_view.R#15) --------------------------
no applicable method for 'img_data_to_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR),
10)) at testthat/test_view.R:15
2: view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR), 10) at d:\RCompile\CRANpkg\local\3.7\radtools.Rcheck\tests\testthat\helper.R:39
3: img_data_to_mat(nifti_data_avg152T1_LR)
== testthat results ===========================================================
OK: 127 SKIPPED: 3 WARNINGS: 15 FAILED: 3
1. Error: NIfTI import (@test_image_import_nifti.R#7)
2. Error: NIfTI metadata (@test_metadata_nifti.R#6)
3. Error: View slice - for CRAN (@test_view.R#15)
Error: testthat unit tests failed
In addition: Warning messages:
1: In dir.create(outdir_nifti, recursive = TRUE) :
'D:\temp\RtmpWcgO7c' already exists
2: In download.file(url, destfile) :
InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
3: In download.file(url, destfile) :
InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
4: In download.file(url, destfile) :
InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 1.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [1m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(radtools)
>
> test_check("radtools")
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-ort.gz'
Content type 'application/x-gzip' length 246877 bytes (241 KB)
==================================================
downloaded 241 KB
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-brain.gz'
Content type 'application/x-gzip' length 261311 bytes (255 KB)
==================================================
downloaded 255 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-head.gz'
Content type 'application/x-gzip' length 70273 bytes (68 KB)
==================================================
downloaded 68 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-knee.gz'
Content type 'application/x-gzip' length 69484 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-8-16x-heart.gz'
Content type 'application/x-gzip' length 337207 bytes (329 KB)
==================================================
downloaded 329 KB
trying URL 'http://barre.nom.fr/medical/samples/files/NM-MONO2-16-13x-heart.gz'
Content type 'application/x-gzip' length 24002 bytes (23 KB)
==================================================
downloaded 23 KB
trying URL 'http://barre.nom.fr/medical/samples/files/US-MONO2-8-8x-execho.gz'
Content type 'application/x-gzip' length 86068 bytes (84 KB)
==================================================
downloaded 84 KB
trying URL 'http://www.dclunie.com/images/charset/charsettests.20070405.tar.bz2'
Content type 'binary/octet-stream' length 6110 bytes
==================================================
downloaded 6110 bytes
trying URL 'http://www.dclunie.com/images/compressed/deflate_tests_release.tar.gz'
Content type 'application/x-gzip' length 65476 bytes (63 KB)
==================================================
downloaded 63 KB
trying URL 'http://www.dclunie.com/images/signedrange/signedrangeimages.tar.bz2'
Content type 'application/x-bzip2' length 278192 bytes (271 KB)
==================================================
downloaded 271 KB
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "/tmp/RtmpIPvEWx/minimal"
Could not read NIfTI-1 object from path /tmp/RtmpIPvEWx/minimal
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "/tmp/RtmpIPvEWx/newsirp_final_XML.nii"
Could not read NIfTI-1 object from path /tmp/RtmpIPvEWx/newsirp_final_XML.nii
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'http://www.neuromorphometrics.com/1103_3.tgz'
Content type 'application/x-tar' length 7286064 bytes (6.9 MB)
==================================================
downloaded 6.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR.nii.gz'
Content type 'application/octet-stream' length 1351404 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR_regToT1.nii.gz'
Content type 'application/octet-stream' length 13690259 bytes (13.1 MB)
==================================================
downloaded 13.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI.nii.gz'
Content type 'application/octet-stream' length 5279 bytes
==================================================
downloaded 5279 bytes
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI_regToT1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 302833 bytes (295 KB)
==================================================
downloaded 295 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1.nii.gz'
Content type 'application/octet-stream' length 3763118 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 6603933 bytes (6.3 MB)
==================================================
downloaded 6.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_brain.nii.gz'
Content type 'application/octet-stream' length 3086068 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_mask.nii.gz'
Content type 'application/octet-stream' length 68732 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/MNI152_T1_1mm_brain.nii.gz'
Content type 'application/octet-stream' length 3219212 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE.nii.gz'
Content type 'application/octet-stream' length 7744679 bytes (7.4 MB)
==================================================
downloaded 7.4 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE_mask.nii.gz'
Content type 'application/octet-stream' length 58905 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/FLIRT_113-01-T2w_regToT1.nii.gz'
Content type 'application/octet-stream' length 29975529 bytes (28.6 MB)
==================================================
downloaded 28.6 MB
── 1. Error: NIfTI import (@test_image_import_nifti.R#7) ──────────────────────
no applicable method for 'img_data_to_3D_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_filtered_func, expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func,
coord_extra_dim = 180)), c(64, 64, 21))) at testthat/test_image_import_nifti.R:7
2: expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)),
c(64, 64, 21)) at /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)
── 2. Error: NIfTI metadata (@test_metadata_nifti.R#6) ────────────────────────
no applicable method for 'num_slices' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, expect_equal(num_slices(nifti_data_avg152T1_LR),
91)) at testthat/test_metadata_nifti.R:6
2: expect_equal(num_slices(nifti_data_avg152T1_LR), 91) at /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: num_slices(nifti_data_avg152T1_LR)
── 3. Error: View slice - for CRAN (@test_view.R#15) ──────────────────────────
no applicable method for 'img_data_to_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR),
10)) at testthat/test_view.R:15
2: view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR), 10) at /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: img_data_to_mat(nifti_data_avg152T1_LR)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 127 SKIPPED: 3 WARNINGS: 15 FAILED: 3
1. Error: NIfTI import (@test_image_import_nifti.R#7)
2. Error: NIfTI metadata (@test_metadata_nifti.R#6)
3. Error: View slice - for CRAN (@test_view.R#15)
Error: testthat unit tests failed
In addition: Warning messages:
1: In dir.create(outdir_nifti, recursive = TRUE) :
'/tmp/RtmpIPvEWx' already exists
2: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz': HTTP status was '502 Bad Gateway'
3: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz': HTTP status was '502 Bad Gateway'
4: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz': HTTP status was '502 Bad Gateway'
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [1m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(radtools)
>
> test_check("radtools")
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-ort.gz'
Content type 'application/gzip' length 246877 bytes (241 KB)
==================================================
downloaded 241 KB
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-brain.gz'
Content type 'application/gzip' length 261311 bytes (255 KB)
==================================================
downloaded 255 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-head.gz'
Content type 'application/gzip' length 70273 bytes (68 KB)
==================================================
downloaded 68 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-knee.gz'
Content type 'application/gzip' length 69484 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-8-16x-heart.gz'
Content type 'application/gzip' length 337207 bytes (329 KB)
==================================================
downloaded 329 KB
trying URL 'http://barre.nom.fr/medical/samples/files/NM-MONO2-16-13x-heart.gz'
Content type 'application/gzip' length 24002 bytes (23 KB)
==================================================
downloaded 23 KB
trying URL 'http://barre.nom.fr/medical/samples/files/US-MONO2-8-8x-execho.gz'
Content type 'application/gzip' length 86068 bytes (84 KB)
==================================================
downloaded 84 KB
trying URL 'http://www.dclunie.com/images/charset/charsettests.20070405.tar.bz2'
Content type 'binary/octet-stream' length 6110 bytes
==================================================
downloaded 6110 bytes
trying URL 'http://www.dclunie.com/images/compressed/deflate_tests_release.tar.gz'
Content type 'application/x-gzip' length 65476 bytes (63 KB)
==================================================
downloaded 63 KB
trying URL 'http://www.dclunie.com/images/signedrange/signedrangeimages.tar.bz2'
Content type 'application/x-bzip2' length 278192 bytes (271 KB)
==================================================
downloaded 271 KB
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "/tmp/RtmphhdikZ/minimal"
Could not read NIfTI-1 object from path /tmp/RtmphhdikZ/minimal
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "/tmp/RtmphhdikZ/newsirp_final_XML.nii"
Could not read NIfTI-1 object from path /tmp/RtmphhdikZ/newsirp_final_XML.nii
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'http://www.neuromorphometrics.com/1103_3.tgz'
Content type 'application/x-tar' length 7286064 bytes (6.9 MB)
==================================================
downloaded 6.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR.nii.gz'
Content type 'application/octet-stream' length 1351404 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR_regToT1.nii.gz'
Content type 'application/octet-stream' length 13690259 bytes (13.1 MB)
==================================================
downloaded 13.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI.nii.gz'
Content type 'application/octet-stream' length 5279 bytes
==================================================
downloaded 5279 bytes
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI_regToT1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 302833 bytes (295 KB)
==================================================
downloaded 295 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1.nii.gz'
Content type 'application/octet-stream' length 3763118 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 6603933 bytes (6.3 MB)
==================================================
downloaded 6.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_brain.nii.gz'
Content type 'application/octet-stream' length 3086068 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_mask.nii.gz'
Content type 'application/octet-stream' length 68732 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/MNI152_T1_1mm_brain.nii.gz'
Content type 'application/octet-stream' length 3219212 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE.nii.gz'
Content type 'application/octet-stream' length 7744679 bytes (7.4 MB)
==================================================
downloaded 7.4 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE_mask.nii.gz'
Content type 'application/octet-stream' length 58905 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/FLIRT_113-01-T2w_regToT1.nii.gz'
Content type 'application/octet-stream' length 29975529 bytes (28.6 MB)
==================================================
downloaded 28.6 MB
── 1. Error: NIfTI import (@test_image_import_nifti.R#7) ──────────────────────
no applicable method for 'img_data_to_3D_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_filtered_func, expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func,
coord_extra_dim = 180)), c(64, 64, 21))) at testthat/test_image_import_nifti.R:7
2: expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)),
c(64, 64, 21)) at /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)
── 2. Error: NIfTI metadata (@test_metadata_nifti.R#6) ────────────────────────
no applicable method for 'num_slices' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, expect_equal(num_slices(nifti_data_avg152T1_LR),
91)) at testthat/test_metadata_nifti.R:6
2: expect_equal(num_slices(nifti_data_avg152T1_LR), 91) at /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: num_slices(nifti_data_avg152T1_LR)
── 3. Error: View slice - for CRAN (@test_view.R#15) ──────────────────────────
no applicable method for 'img_data_to_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR),
10)) at testthat/test_view.R:15
2: view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR), 10) at /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/radtools.Rcheck/tests/testthat/helper.R:39
3: img_data_to_mat(nifti_data_avg152T1_LR)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 127 SKIPPED: 3 WARNINGS: 15 FAILED: 3
1. Error: NIfTI import (@test_image_import_nifti.R#7)
2. Error: NIfTI metadata (@test_metadata_nifti.R#6)
3. Error: View slice - for CRAN (@test_view.R#15)
Error: testthat unit tests failed
In addition: Warning messages:
1: In dir.create(outdir_nifti, recursive = TRUE) :
'/tmp/RtmphhdikZ' already exists
2: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz': HTTP status was '502 Bad Gateway'
3: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz': HTTP status was '502 Bad Gateway'
4: In download.file(url, destfile) :
cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz': HTTP status was '502 Bad Gateway'
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.0.6
Check: tests
Result: ERROR
Running 'testthat.R' [14m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(radtools)
>
> test_check("radtools")
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-ort.gz'
Content type 'application/x-gzip' length 246877 bytes (241 KB)
==================================================
downloaded 241 KB
trying URL 'http://barre.nom.fr/medical/samples/files/CT-MONO2-16-brain.gz'
Content type 'application/x-gzip' length 261311 bytes (255 KB)
==================================================
downloaded 255 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-head.gz'
Content type 'application/x-gzip' length 70273 bytes (68 KB)
==================================================
downloaded 68 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-16-knee.gz'
Content type 'application/x-gzip' length 69484 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'http://barre.nom.fr/medical/samples/files/MR-MONO2-8-16x-heart.gz'
Content type 'application/x-gzip' length 337207 bytes (329 KB)
==================================================
downloaded 329 KB
trying URL 'http://barre.nom.fr/medical/samples/files/NM-MONO2-16-13x-heart.gz'
Content type 'application/x-gzip' length 24002 bytes (23 KB)
==================================================
downloaded 23 KB
trying URL 'http://barre.nom.fr/medical/samples/files/US-MONO2-8-8x-execho.gz'
Content type 'application/x-gzip' length 86068 bytes (84 KB)
==================================================
downloaded 84 KB
trying URL 'http://www.dclunie.com/images/charset/charsettests.20070405.tar.bz2'
Content type 'binary/octet-stream' length 6110 bytes
==================================================
downloaded 6110 bytes
trying URL 'http://www.dclunie.com/images/compressed/deflate_tests_release.tar.gz'
Content type 'application/x-gzip' length 65476 bytes (63 KB)
==================================================
downloaded 63 KB
trying URL 'http://www.dclunie.com/images/signedrange/signedrangeimages.tar.bz2'
Content type 'application/x-bzip2' length 278192 bytes (271 KB)
==================================================
downloaded 271 KB
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.img.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.hdr.gz
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/minimal.img.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "D:/temp/RtmpikuZTG/minimal"
Could not read NIfTI-1 object from path D:/temp/RtmpikuZTG/minimal
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/sirp_fmri_study_ver4.tar.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: File(s) not found!
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = "D:/temp/RtmpikuZTG/newsirp_final_XML.nii"
Could not read NIfTI-1 object from path D:/temp/RtmpikuZTG/newsirp_final_XML.nii
trying URL 'https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz'
Could not download file from url https://nifti.nimh.nih.gov/nifti-1/data/zstat1.nii.gz
Error raised by oro.nifti::readNIfTI
Message from oro.nifti: non-character argument
On expression: oro.nifti::readNIfTI(file, ...)
With file(s) = ""
Could not read NIfTI-1 object from path
trying URL 'http://www.neuromorphometrics.com/1103_3.tgz'
Content type 'application/x-tar' length 7286064 bytes (6.9 MB)
==================================================
downloaded 6.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR.nii.gz'
Content type 'application/octet-stream' length 1351404 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/FLAIR_regToT1.nii.gz'
Content type 'application/octet-stream' length 13690259 bytes (13.1 MB)
==================================================
downloaded 13.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI.nii.gz'
Content type 'application/octet-stream' length 5279 bytes
==================================================
downloaded 5279 bytes
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/ROI_regToT1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 302833 bytes (295 KB)
==================================================
downloaded 295 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1.nii.gz'
Content type 'application/octet-stream' length 3763118 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/BRAINIX/NIfTI/T1_SyNtoMNI.nii.gz'
Content type 'application/octet-stream' length 6603933 bytes (6.3 MB)
==================================================
downloaded 6.3 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_brain.nii.gz'
Content type 'application/octet-stream' length 3086068 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/JHU_MNI_SS_T1_mask.nii.gz'
Content type 'application/octet-stream' length 68732 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/Template/MNI152_T1_1mm_brain.nii.gz'
Content type 'application/octet-stream' length 3219212 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE.nii.gz'
Content type 'application/octet-stream' length 7744679 bytes (7.4 MB)
==================================================
downloaded 7.4 MB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/113-01-MPRAGE_mask.nii.gz'
Content type 'application/octet-stream' length 58905 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://github.com/muschellij2/Neurohacking_data/raw/master/kirby21/visit_1/113/FLIRT_113-01-T2w_regToT1.nii.gz'
Content type 'application/octet-stream' length 29975529 bytes (28.6 MB)
==================================================
downloaded 28.6 MB
-- 1. Error: NIfTI import (@test_image_import_nifti.R#7) ----------------------
no applicable method for 'img_data_to_3D_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_filtered_func, expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func,
coord_extra_dim = 180)), c(64, 64, 21))) at testthat/test_image_import_nifti.R:7
2: expect_equal(dim(img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)),
c(64, 64, 21)) at d:\RCompile\CRANpkg\local\3.5\radtools.Rcheck\tests\testthat\helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: img_data_to_3D_mat(nifti_data_filtered_func, coord_extra_dim = 180)
-- 2. Error: NIfTI metadata (@test_metadata_nifti.R#6) ------------------------
no applicable method for 'num_slices' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, expect_equal(num_slices(nifti_data_avg152T1_LR),
91)) at testthat/test_metadata_nifti.R:6
2: expect_equal(num_slices(nifti_data_avg152T1_LR), 91) at d:\RCompile\CRANpkg\local\3.5\radtools.Rcheck\tests\testthat\helper.R:39
3: quasi_label(enquo(object), label, arg = "object")
4: eval_bare(get_expr(quo), get_env(quo))
5: num_slices(nifti_data_avg152T1_LR)
-- 3. Error: View slice - for CRAN (@test_view.R#15) --------------------------
no applicable method for 'img_data_to_mat' applied to an object of class "NULL"
1: expression_try(nifti_data_avg152T1_LR, view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR),
10)) at testthat/test_view.R:15
2: view_slice_mat(img_data_to_mat(nifti_data_avg152T1_LR), 10) at d:\RCompile\CRANpkg\local\3.5\radtools.Rcheck\tests\testthat\helper.R:39
3: img_data_to_mat(nifti_data_avg152T1_LR)
== testthat results ===========================================================
OK: 127 SKIPPED: 3 WARNINGS: 15 FAILED: 3
1. Error: NIfTI import (@test_image_import_nifti.R#7)
2. Error: NIfTI metadata (@test_metadata_nifti.R#6)
3. Error: View slice - for CRAN (@test_view.R#15)
Error: testthat unit tests failed
In addition: Warning messages:
1: In dir.create(outdir_nifti, recursive = TRUE) :
'D:\temp\RtmpikuZTG' already exists
2: In download.file(url, destfile) :
InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
3: In download.file(url, destfile) :
InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
4: In download.file(url, destfile) :
InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64