Till Soerensen
| Snapshot Date: 2025-10-06 13:40 -0400 (Mon, 06 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/immunoClust |
| git_branch: RELEASE_3_21 |
| git_last_commit: c20d14f |
| git_last_commit_date: 2025-04-15 10:48:52 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-09 11:41 -0400 (Thu, 09 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1040/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| immunoClust 1.40.0 (landing page) Till Soerensen
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the immunoClust package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/immunoClust.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: immunoClust |
| Version: 1.40.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data immunoClust |
| StartedAt: 2025-10-07 01:50:57 -0000 (Tue, 07 Oct 2025) |
| EndedAt: 2025-10-07 01:54:59 -0000 (Tue, 07 Oct 2025) |
| EllapsedTime: 241.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data immunoClust
###
##############################################################################
##############################################################################
* checking for file ‘immunoClust/DESCRIPTION’ ... OK
* preparing ‘immunoClust’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘immunoClust.Rnw’ using Sweave
Loading required package: flowCore
filtered from above:318
filtered from below:0
cluster 1(N=151) has 2 sub-cluster at 2 (19), ICL=149<>26
split 1 into 2 clusters
cluster 1(N=151) has 2 sub-cluster at 2 (19), ICL=0<>26
Model Refinement takes 0.033 mins(max 1: 0.033)
Fit Model 1 of (6/10) K=1->2 N=302
EM 2 takes 0 mins, 10 iterations
cluster 2(N=77) has 2 sub-cluster at 2 (7), ICL=105<>30
split 2 into 2 clusters
cluster 1(N=226) has 2 sub-cluster at 2 (11), ICL=54<>30
split 1 into 2 clusters
cluster 1(N=226) has 2 sub-cluster at 2 (11), ICL=0<>30
Model Refinement takes 0.05 mins(max 1: 0.033)
Fit Model 2 of (6/10) K=2->4 N=605
EM 4 takes 0 mins, 8 iterations
cluster 3(N=96) has 2 sub-cluster at 2 (6), ICL=63<>34
split 3 into 2 clusters
cluster 2(N=44) has 2 sub-cluster at 2 (6), ICL=43<>34
split 2 into 2 clusters
cluster 1(N=407) has 3 sub-cluster at 3 (12), ICL=5.7<>34
cluster 4(N=60) has 2 sub-cluster at 3 (13), ICL=1.1<>34
cluster 1(N=407) has 3 sub-cluster at 3 (12), ICL=0<>34
Model Refinement takes 0.067 mins(max 1: 0.017)
Fit Model 3 of (6/10) K=4->6 N=1210
EM 6 takes 0 mins, 11 iterations
cluster 4(N=152) has 7 sub-cluster at 7 (38), ICL=16<>37
cluster 2(N=66) has 3 sub-cluster at 3 (14), ICL=16<>37
cluster 6(N=106) has 2 sub-cluster at 2 (5), ICL=15<>37
cluster 5(N=43) has 3 sub-cluster at 3 (16), ICL=13<>37
cluster 3(N=13) has 2 sub-cluster at 2 (100), ICL=7.3<>37
cluster 1(N=832) has 4 sub-cluster at 4 (9), ICL=1.5<>37
cluster 1(N=832) has 4 sub-cluster at 4 (9), ICL=0<>37
Model Refinement takes 0.083 mins(max 1: 0.033)
Fit Model 4 of (6/10) K=6->6 N=2420
EM 6 takes 0.017 mins, 6 iterations
cluster 6(N=251) has 3 sub-cluster at 3 (22), ICL=34<>41
cluster 1(N=1654) has 2 sub-cluster at 2 (6), ICL=26<>41
cluster 5(N=89) has 5 sub-cluster at 5 (18), ICL=21<>41
cluster 4(N=264) has 7 sub-cluster at 7 (37), ICL=15<>41
cluster 2(N=146) has 3 sub-cluster at 3 (10), ICL=14<>41
cluster 3(N=26) has 2 sub-cluster at 2 (100), ICL=5.6<>41
cluster 1(N=1654) has 2 sub-cluster at 2 (6), ICL=0<>41
Model Refinement takes 0.17 mins(max 1: 0.067)
Fit Model 5 of (6/10) K=6->6 N=4841
EM 6 takes 0.017 mins, 6 iterations
cluster 6(N=491) has 2 sub-cluster at 2 (13), ICL=136<>45
split 6 into 2 clusters
cluster 1(N=3275) has 3 sub-cluster at 3 (9), ICL=71<>45
split 1 into 3 clusters
cluster 3(N=78) has 6 sub-cluster at 7 (56), ICL=46<>45
split 3 into 6 clusters
cluster 5(N=185) has 2 sub-cluster at 2 (27), ICL=25<>45
cluster 2(N=275) has 4 sub-cluster at 4 (40), ICL=23<>45
cluster 4(N=565) has 2 sub-cluster at 3 (5), ICL=9.9<>45
cluster 1(N=3275) has 3 sub-cluster at 3 (9), ICL=0<>45
Model Refinement takes 0.22 mins(max 1: 0.083)
Fit Model 6 of (6/10) K=6->14 N=9682
EM 14 takes 0.05 mins, 22 iterations
Warning in cell.TestSubCluster(x, as.matrix(y[cinc, ]), t, k, J = J, B = B, :
singularity in cluster 5
cluster 1(N=372) has 2 sub-cluster at 2 (6), ICL=129<>48
split 1 into 2 clusters
cluster 4(N=561) has 3 sub-cluster at 3 (8), ICL=63<>48
split 4 into 3 clusters
cluster 8(N=11) has 2 sub-cluster at 2 (100), ICL=40<>48
cluster 12(N=389) has 3 sub-cluster at 3 (34), ICL=38<>48
cluster 14(N=60) has 2 sub-cluster at 2 (10), ICL=29<>48
cluster 13(N=909) has 4 sub-cluster at 4 (15), ICL=22<>48
cluster 6(N=77) has 6 sub-cluster at 6 (20), ICL=16<>48
cluster 10(N=264) has 2 sub-cluster at 3 (6), ICL=9.5<>48
cluster 9(N=15) has 2 sub-cluster at 2 (100), ICL=6.7<>48
cluster 1(N=372) has 2 sub-cluster at 2 (6), ICL=0<>48
Model Refinement takes 0.42 mins(max 2: 0.1)
Fit Model 7 of (6/10) K=14->17 N=9682
EM 17 takes 0 mins, 7 iterations
Warning in cell.TestSubCluster(x, as.matrix(y[cinc, ]), t, k, J = J, B = B, :
singularity in cluster 8
cluster 15(N=389) has 2 sub-cluster at 2 (6), ICL=38<>48
cluster 16(N=898) has 3 sub-cluster at 3 (9), ICL=29<>48
cluster 17(N=60) has 2 sub-cluster at 2 (10), ICL=29<>48
cluster 7(N=90) has 3 sub-cluster at 3 (15), ICL=21<>48
cluster 5(N=363) has 7 sub-cluster at 8 (28), ICL=15<>48
cluster 13(N=330) has 6 sub-cluster at 6 (46), ICL=15<>48
cluster 2(N=74) has 3 sub-cluster at 4 (48), ICL=13<>48
cluster 11(N=11) has 2 sub-cluster at 2 (100), ICL=13<>48
cluster 9(N=79) has 5 sub-cluster at 5 (20), ICL=12<>48
cluster 6(N=182) has 7 sub-cluster at 8 (35), ICL=11<>48
cluster 12(N=15) has 2 sub-cluster at 2 (100), ICL=6<>48
cluster 1(N=307) has 2 sub-cluster at 2 (11), ICL=4.3<>48
cluster 1(N=307) has 2 sub-cluster at 2 (11), ICL=0<>48
Model Refinement takes 0.47 mins(max 3: 0.083)
Fit Model 8 of (6/10) K=17->17 N=9682
EM 17 takes 0 mins, 3 iterations
Process completed at8
Major Iteration (Trans) (6/4) takes 1.6 mins
filtered from above:318
filtered from below:0
cluster 1(N=151) has 3 sub-cluster at 3 (8), ICL=150<>22
split 1 into 3 clusters
cluster 1(N=151) has 3 sub-cluster at 3 (8), ICL=0<>22
Model Refinement takes 0.033 mins(max 1: 0.033)
Fit Model 1 of (6/10) K=1->3 N=302
EM 3 takes 0 mins, 9 iterations
cluster 2(N=63) has 2 sub-cluster at 2 (8), ICL=50<>25
split 2 into 2 clusters
cluster 3(N=25) has 2 sub-cluster at 2 (100), ICL=21<>25
cluster 1(N=216) has 3 sub-cluster at 3 (18), ICL=14<>25
cluster 1(N=216) has 3 sub-cluster at 3 (18), ICL=0<>25
Model Refinement takes 0.033 mins(max 1: 0.017)
Fit Model 2 of (6/10) K=3->4 N=605
EM 4 takes 0 mins, 9 iterations
cluster 1(N=418) has 2 sub-cluster at 2 (9), ICL=78<>28
split 1 into 2 clusters
cluster 3(N=69) has 2 sub-cluster at 2 (13), ICL=40<>28
split 3 into 2 clusters
cluster 4(N=58) has 2 sub-cluster at 2 (65), ICL=5.5<>28
cluster 2(N=61) has 2 sub-cluster at 2 (100), ICL=3.9<>28
cluster 1(N=418) has 2 sub-cluster at 2 (9), ICL=0<>28
Model Refinement takes 0.05 mins(max 1: 0.033)
Fit Model 3 of (6/10) K=4->6 N=1210
EM 6 takes 0.017 mins, 8 iterations
cluster 2(N=31) has 2 sub-cluster at 2 (100), ICL=31<>31
cluster 4(N=63) has 3 sub-cluster at 3 (10), ICL=19<>31
cluster 5(N=51) has 2 sub-cluster at 2 (11), ICL=18<>31
cluster 3(N=157) has 7 sub-cluster at 7 (30), ICL=17<>31
cluster 6(N=128) has 2 sub-cluster at 2 (9), ICL=9.8<>31
cluster 1(N=792) has 3 sub-cluster at 3 (6), ICL=4<>31
cluster 1(N=792) has 3 sub-cluster at 3 (6), ICL=0<>31
Model Refinement takes 0.083 mins(max 1: 0.017)
Fit Model 4 of (6/10) K=6->6 N=2420
EM 6 takes 0 mins, 9 iterations
cluster 2(N=127) has 2 sub-cluster at 2 (7), ICL=71<>34
split 2 into 2 clusters
cluster 6(N=218) has 2 sub-cluster at 2 (8), ICL=56<>34
split 6 into 2 clusters
cluster 5(N=103) has 2 sub-cluster at 2 (9), ICL=30<>34
cluster 3(N=268) has 2 sub-cluster at 2 (7), ICL=27<>34
cluster 4(N=135) has 4 sub-cluster at 4 (11), ICL=21<>34
cluster 2(N=127) has 2 sub-cluster at 2 (7), ICL=0<>34
Model Refinement takes 0.2 mins(max 1: 0.083)
Fit Model 5 of (6/10) K=6->8 N=4841
EM 8 takes 0.017 mins, 6 iterations
cluster 3(N=95) has 2 sub-cluster at 2 (7), ICL=65<>37
split 3 into 2 clusters
cluster 8(N=25) has 2 sub-cluster at 2 (100), ICL=43<>37
split 8 into 2 clusters
cluster 5(N=286) has 3 sub-cluster at 3 (8), ICL=37<>37
cluster 4(N=583) has 2 sub-cluster at 2 (8), ICL=35<>37
cluster 6(N=186) has 7 sub-cluster at 8 (41), ICL=23<>37
cluster 2(N=159) has 4 sub-cluster at 5 (40), ICL=16<>37
cluster 7(N=443) has 7 sub-cluster at 7 (29), ICL=15<>37
cluster 2(N=159) has 4 sub-cluster at 5 (40), ICL=0<>37
Model Refinement takes 0.22 mins(max 1: 0.083)
Fit Model 6 of (6/10) K=8->10 N=9682
EM 9 takes 0.017 mins, 5 iterations
cluster 6(N=557) has 3 sub-cluster at 3 (11), ICL=69<>40
split 6 into 3 clusters
cluster 8(N=916) has 3 sub-cluster at 3 (10), ICL=55<>40
split 8 into 3 clusters
cluster 3(N=153) has 4 sub-cluster at 4 (10), ICL=43<>40
split 3 into 4 clusters
cluster 5(N=1122) has 2 sub-cluster at 2 (6), ICL=43<>40
split 5 into 2 clusters
cluster 7(N=392) has 3 sub-cluster at 3 (33), ICL=41<>40
split 7 into 3 clusters
cluster 2(N=314) has 5 sub-cluster at 6 (41), ICL=5.3<>40
cluster 4(N=75) has 3 sub-cluster at 4 (12), ICL=2.4<>40
cluster 2(N=314) has 5 sub-cluster at 6 (41), ICL=0<>40
Model Refinement takes 0.3 mins(max 1: 0.1)
Fit Model 7 of (6/10) K=9->19 N=9682
EM 19 takes 0.017 mins, 4 iterations
cluster 4(N=22) has 2 sub-cluster at 2 (9), ICL=20<>40
cluster 12(N=77) has 2 sub-cluster at 2 (17), ICL=20<>40
cluster 3(N=86) has 4 sub-cluster at 4 (28), ICL=17<>40
cluster 14(N=120) has 4 sub-cluster at 5 (42), ICL=16<>40
cluster 7(N=74) has 3 sub-cluster at 4 (45), ICL=15<>40
cluster 10(N=358) has 4 sub-cluster at 4 (14), ICL=13<>40
cluster 15(N=132) has 5 sub-cluster at 6 (22), ICL=12<>40
cluster 5(N=23) has 2 sub-cluster at 2 (4), ICL=10<>40
cluster 2(N=308) has 2 sub-cluster at 2 (7), ICL=9<>40
cluster 11(N=181) has 4 sub-cluster at 5 (17), ICL=8.7<>40
cluster 18(N=50) has 2 sub-cluster at 2 (100), ICL=6.9<>40
cluster 16(N=384) has 7 sub-cluster at 7 (28), ICL=0.35<>40
cluster 2(N=308) has 2 sub-cluster at 2 (7), ICL=0<>40
Model Refinement takes 0.42 mins(max 1: 0.083)
Fit Model 8 of (6/10) K=19->19 N=9682
EM 19 takes 0 mins, 3 iterations
Process completed at8
Major Iteration (Trans) (6/4) takes 1.4 mins
Fit Model 1 of 10 with 8 clusters
=> results in 8 clusters
Fit Model 2 of 10 with 21 clusters
=> results in 13 clusters
Fit Model 3 of 10 with 23 clusters
=> results in 19 clusters
Fit Model 4 of 10 with 26 clusters
=> results in 21 clusters
Fit Model 5 of 10 with 25 clusters
=> results in 21 clusters
Error: processing vignette 'immunoClust.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'immunoClust.tex' failed.
LaTeX errors:
! LaTeX Error: File `inputenx.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.15 ^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘immunoClust.Rnw’
SUMMARY: processing the following file failed:
‘immunoClust.Rnw’
Error: Vignette re-building failed.
Execution halted