Last updated on 2025-02-21 17:50:37 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 66.32 | 901.71 | 968.03 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 63.59 | 682.27 | 745.86 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 1420.34 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 1449.51 | ERROR | |||
| r-devel-macos-arm64 | 0.1.0 | 5.00 | ERROR | |||
| r-devel-macos-x86_64 | 0.1.0 | 6.00 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.0 | 82.00 | 839.00 | 921.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 64.83 | 883.56 | 948.39 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 66.92 | 879.07 | 945.99 | OK | |
| r-release-macos-arm64 | 0.1.0 | 10.00 | ERROR | |||
| r-release-macos-x86_64 | 0.1.0 | 502.00 | NOTE | |||
| r-release-windows-x86_64 | 0.1.0 | 86.00 | 875.00 | 961.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | 461.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.1.0 | 11.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.1.0 | 93.00 | 1004.00 | 1097.00 | ERROR |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘CAESAR.Suite-Ex.R’ failed
The error most likely occurred in:
> ### Name: CoUMAP
> ### Title: Co-embedding UMAP for Genes and Cells in a Seurat Object
> ### Aliases: CoUMAP
>
> ### ** Examples
>
> data(toydata)
>
> seu <- toydata$seu
>
> seu <- CoUMAP(seu, gene.set = rownames(seu))
Error in min(nrow(X), na.rm = col(X)) :
'length = 40100' in coercion to 'logical(1)'
Calls: CoUMAP ... <Anonymous> -> .local -> do.call -> <Anonymous> -> uwot
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘STMOB.Rmd’ using rmarkdown
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_ST.rda?raw=true'
Content type 'application/octet-stream' length 5988380 bytes (5.7 MB)
==================================================
downloaded 5.7 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_scRNA.rda?raw=true'
Content type 'application/octet-stream' length 48066404 bytes (45.8 MB)
==================================================
downloaded 45.8 MB
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Progress: ────────────────────────────────────── 100%
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Progress: ──────────────────────────────────────────────────────────────── 100%** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-12-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 126368 bytes
Input file size = 126626 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 92863
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 92863
Output IDAT size = 92863 bytes (33505 bytes decrease)
Output file size = 92941 bytes (33685 bytes = 26.60% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-13-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 127839 bytes
Input file size = 128097 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814
Output IDAT size = 93814 bytes (34025 bytes decrease)
Output file size = 93892 bytes (34205 bytes = 26.70% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-14-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 127839 bytes
Input file size = 128097 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814
Output IDAT size = 93814 bytes (34025 bytes decrease)
Output file size = 93892 bytes (34205 bytes = 26.70% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-15-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 91989 bytes
Input file size = 92199 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66560
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66560
Output IDAT size = 66560 bytes (25429 bytes decrease)
Output file size = 66638 bytes (25561 bytes = 27.72% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-16-1.png
844x864 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 188968 bytes
Input file size = 189322 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 168348
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 168348
Output IDAT size = 168348 bytes (20620 bytes decrease)
Output file size = 168426 bytes (20896 bytes = 11.04% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-19-1.png
844x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49375 bytes
Input file size = 49525 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38960
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38960
Output IDAT size = 38960 bytes (10415 bytes decrease)
Output file size = 39038 bytes (10487 bytes = 21.18% decrease)
Quitting from lines 267-282 [unnamed-chunk-20] (STMOB.Rmd)
Error: processing vignette 'STMOB.Rmd' failed with diagnostics:
'length = 14600' in coercion to 'logical(1)'
--- failed re-building ‘STMOB.Rmd’
--- re-building ‘XeniumBC.Rmd’ using rmarkdown
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_scRNAList.rda?raw=true'
Content type 'application/octet-stream' length 2310272 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_XeniumList.rda?raw=true'
Content type 'application/octet-stream' length 1256437 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_feature_imgList.rda?raw=true'
Content type 'application/octet-stream' length 12559173 bytes (12.0 MB)
==================================================
downloaded 12.0 MB
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Progress: ───── 100%
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Progress: ──────────────────────────────────────────────────────────────── 100%** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-12-1.png
1152x1512 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 527131 bytes
Input file size = 527977 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 365220
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 365220
Output IDAT size = 365220 bytes (161911 bytes decrease)
Output file size = 365298 bytes (162679 bytes = 30.81% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-13-1.png
1152x1512 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 404815 bytes
Input file size = 405481 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 284971
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 284971
Output IDAT size = 284971 bytes (119844 bytes decrease)
Output file size = 285049 bytes (120432 bytes = 29.70% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-16-1.png
1152x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 137347 bytes
Input file size = 137617 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 109537
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 109537
Output IDAT size = 109537 bytes (27810 bytes decrease)
Output file size = 109615 bytes (28002 bytes = 20.35% decrease)
Quitting from lines 287-306 [unnamed-chunk-17] (XeniumBC.Rmd)
Error: processing vignette 'XeniumBC.Rmd' failed with diagnostics:
'length = 151350' in coercion to 'logical(1)'
--- failed re-building ‘XeniumBC.Rmd’
SUMMARY: processing the following files failed:
‘STMOB.Rmd’ ‘XeniumBC.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘STMOB.Rmd’ using rmarkdown
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_ST.rda?raw=true'
Content type 'application/octet-stream' length 5988380 bytes (5.7 MB)
==================================================
downloaded 5.7 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_scRNA.rda?raw=true'
Content type 'application/octet-stream' length 48066404 bytes (45.8 MB)
==================================================
downloaded 45.8 MB
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Progress: ────────────────────────────── 100%
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Progress: ─────────────────────────────────────────────────────────────── 100%
Progress: ──────────────────────────────────────────────────────────────── 100%** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-12-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 126368 bytes
Input file size = 126626 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 92863
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 92863
Output IDAT size = 92863 bytes (33505 bytes decrease)
Output file size = 92941 bytes (33685 bytes = 26.60% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-13-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 127839 bytes
Input file size = 128097 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814
Output IDAT size = 93814 bytes (34025 bytes decrease)
Output file size = 93892 bytes (34205 bytes = 26.70% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-14-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 127839 bytes
Input file size = 128097 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814
Output IDAT size = 93814 bytes (34025 bytes decrease)
Output file size = 93892 bytes (34205 bytes = 26.70% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-15-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 91989 bytes
Input file size = 92199 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66560
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66560
Output IDAT size = 66560 bytes (25429 bytes decrease)
Output file size = 66638 bytes (25561 bytes = 27.72% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-16-1.png
844x864 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 188968 bytes
Input file size = 189322 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 168348
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 168348
Output IDAT size = 168348 bytes (20620 bytes decrease)
Output file size = 168426 bytes (20896 bytes = 11.04% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-19-1.png
844x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49375 bytes
Input file size = 49525 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38960
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38960
Output IDAT size = 38960 bytes (10415 bytes decrease)
Output file size = 39038 bytes (10487 bytes = 21.18% decrease)
Quitting from lines 267-282 [unnamed-chunk-20] (STMOB.Rmd)
Error: processing vignette 'STMOB.Rmd' failed with diagnostics:
'length = 14600' in coercion to 'logical(1)'
--- failed re-building ‘STMOB.Rmd’
--- re-building ‘XeniumBC.Rmd’ using rmarkdown
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_scRNAList.rda?raw=true'
Content type 'application/octet-stream' length 2310272 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_XeniumList.rda?raw=true'
Content type 'application/octet-stream' length 1256437 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_feature_imgList.rda?raw=true'
Content type 'application/octet-stream' length 12559173 bytes (12.0 MB)
==================================================
downloaded 12.0 MB
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Progress: ────── 100%
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Progress: ──────────────────────────────────────────────────────────────── 100%** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-12-1.png
1152x1512 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 527131 bytes
Input file size = 527977 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 365220
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 365220
Output IDAT size = 365220 bytes (161911 bytes decrease)
Output file size = 365298 bytes (162679 bytes = 30.81% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-13-1.png
1152x1512 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 404815 bytes
Input file size = 405481 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 284971
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 284971
Output IDAT size = 284971 bytes (119844 bytes decrease)
Output file size = 285049 bytes (120432 bytes = 29.70% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-16-1.png
1152x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 137347 bytes
Input file size = 137617 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 109537
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 109537
Output IDAT size = 109537 bytes (27810 bytes decrease)
Output file size = 109615 bytes (28002 bytes = 20.35% decrease)
Quitting from lines 287-306 [unnamed-chunk-17] (XeniumBC.Rmd)
Error: processing vignette 'XeniumBC.Rmd' failed with diagnostics:
'length = 151350' in coercion to 'logical(1)'
--- failed re-building ‘XeniumBC.Rmd’
SUMMARY: processing the following files failed:
‘STMOB.Rmd’ ‘XeniumBC.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘ProFAST’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-devel-macos-arm64, r-devel-macos-x86_64, r-release-macos-arm64, r-oldrel-macos-x86_64
Version: 0.1.0
Check: installed package size
Result: NOTE
installed size is 8.4Mb
sub-directories of 1Mb or more:
data 1.4Mb
doc 1.1Mb
libs 5.5Mb
Flavors: r-release-macos-x86_64, r-oldrel-macos-arm64
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'STMOB.Rmd' using rmarkdown
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_ST.rda?raw=true'
Content type 'application/octet-stream' length 5988380 bytes (5.7 MB)
==================================================
downloaded 5.7 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_scRNA.rda?raw=true'
Content type 'application/octet-stream' length 48066404 bytes (45.8 MB)
=================
downloaded 15.6 MB
Quitting from lines 29-42 [unnamed-chunk-2] (STMOB.Rmd)
Error: processing vignette 'STMOB.Rmd' failed with diagnostics:
download from 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_scRNA.rda?raw=true' failed
--- failed re-building 'STMOB.Rmd'
--- re-building 'XeniumBC.Rmd' using rmarkdown
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_scRNAList.rda?raw=true'
Content type 'application/octet-stream' length 2310272 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_XeniumList.rda?raw=true'
Content type 'application/octet-stream' length 1256437 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_feature_imgList.rda?raw=true'
Content type 'application/octet-stream' length 12559173 bytes (12.0 MB)
==================================================
downloaded 12.0 MB
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building 'XeniumBC.Rmd'
SUMMARY: processing the following file failed:
'STMOB.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64