- using R Under development (unstable) (2025-03-10 r87922)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.7 (1+b1)
Debian flang-new version 19.1.7 (1+b1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘CAESAR.Suite’ version ‘0.2.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘CAESAR.Suite’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘Debian clang version 19.1.7 (1+b1)’
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [23s/28s] OK
- checking whether the package can be loaded with stated dependencies ... [20s/26s] OK
- checking whether the package can be unloaded cleanly ... [20s/24s] OK
- checking whether the namespace can be loaded with stated dependencies ... [20s/24s] OK
- checking whether the namespace can be unloaded cleanly ... [22s/27s] OK
- checking loading without being on the library search path ... [22s/27s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [99s/124s] OK
- checking Rd files ... [0s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [4s/5s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [51s/65s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CoUMAP.plot 5.932 0.002 7.033
CoUMAP 5.215 0.033 6.963
CAESAR.CTDEP 3.907 0.430 5.625
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [283s/302s] 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%
Progress: ──────────────────────────────────────────── 100%
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Progress: ─────────────────────────────────────────────────────────────── 100%
Progress: ──────────────────────────────────────────────────────────────── 100%** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 126860 bytes
Input file size = 127118 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96729
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 = 96729
Output IDAT size = 96729 bytes (30131 bytes decrease)
Output file size = 96807 bytes (30311 bytes = 23.84% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 128341 bytes
Input file size = 128599 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97991
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 = 97991
Output IDAT size = 97991 bytes (30350 bytes decrease)
Output file size = 98069 bytes (30530 bytes = 23.74% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 128341 bytes
Input file size = 128599 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97991
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 = 97991
Output IDAT size = 97991 bytes (30350 bytes decrease)
Output file size = 98069 bytes (30530 bytes = 23.74% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 92821 bytes
Input file size = 93031 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 68226
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 = 68226
Output IDAT size = 68226 bytes (24595 bytes decrease)
Output file size = 68304 bytes (24727 bytes = 26.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 189490 bytes
Input file size = 189844 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 170046
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 = 170046
Output IDAT size = 170046 bytes (19444 bytes decrease)
Output file size = 170124 bytes (19720 bytes = 10.39% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 49756 bytes
Input file size = 49906 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41497
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 = 41497
Output IDAT size = 41497 bytes (8259 bytes decrease)
Output file size = 41575 bytes (8331 bytes = 16.69% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-20-1.png
844x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 63220 bytes
Input file size = 63382 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 49156
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 = 49156
Output IDAT size = 49156 bytes (14064 bytes decrease)
Output file size = 49234 bytes (14148 bytes = 22.32% decrease)
--- finished 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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 529798 bytes
Input file size = 530644 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 381671
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 = 381671
Output IDAT size = 381671 bytes (148127 bytes decrease)
Output file size = 381749 bytes (148895 bytes = 28.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 407870 bytes
Input file size = 408536 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 290562
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 = 290562
Output IDAT size = 290562 bytes (117308 bytes decrease)
Output file size = 290640 bytes (117896 bytes = 28.86% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 138203 bytes
Input file size = 138473 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 113268
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 = 113268
Output IDAT size = 113268 bytes (24935 bytes decrease)
Output file size = 113346 bytes (25127 bytes = 18.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-17-1.png
1152x1512 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 303779 bytes
Input file size = 304301 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 230022
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 = 230022
Output IDAT size = 230022 bytes (73757 bytes decrease)
Output file size = 230100 bytes (74201 bytes = 24.38% decrease)
Quitting from lines 323-331 [unnamed-chunk-19] (XeniumBC.Rmd)
Error: processing vignette 'XeniumBC.Rmd' failed with diagnostics:
attempt to set 'colnames' on an object with less than two dimensions
--- failed re-building ‘XeniumBC.Rmd’
SUMMARY: processing the following file failed:
‘XeniumBC.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [5s/6s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR