Till Soerensen
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 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 2025-09-25 11:42 -0400 (Thu, 25 Sep 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" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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: 2025-09-23 02:31:47 -0000 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 02:37:01 -0000 (Tue, 23 Sep 2025) |
| EllapsedTime: 314.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### 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 (7), ICL=154<>26
split 1 into 2 clusters
cluster 1(N=151) has 2 sub-cluster at 2 (7), ICL=0<>26
Model Refinement takes 0.017 mins(max 1: 0.017)
Fit Model 1 of (6/10) K=1->2 N=302
EM 2 takes 0 mins, 8 iterations
cluster 2(N=105) has 3 sub-cluster at 3 (8), ICL=114<>30
split 2 into 3 clusters
cluster 1(N=200) has 2 sub-cluster at 2 (7), ICL=25<>30
cluster 1(N=200) has 2 sub-cluster at 2 (7), 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, 7 iterations
cluster 1(N=430) has 2 sub-cluster at 2 (6), ICL=58<>34
split 1 into 2 clusters
cluster 4(N=72) has 5 sub-cluster at 5 (14), ICL=37<>34
split 4 into 5 clusters
cluster 3(N=51) has 3 sub-cluster at 3 (16), ICL=26<>34
cluster 2(N=54) has 4 sub-cluster at 6 (33), ICL=24<>34
cluster 1(N=430) has 2 sub-cluster at 2 (6), ICL=0<>34
Model Refinement takes 0.083 mins(max 1: 0.033)
Fit Model 3 of (6/10) K=4->9 N=1210
EM 7 takes 0 mins, 12 iterations
cluster 4(N=134) has 2 sub-cluster at 2 (6), ICL=72<>37
split 4 into 2 clusters
cluster 6(N=55) has 4 sub-cluster at 4 (29), ICL=23<>37
cluster 2(N=39) has 3 sub-cluster at 3 (9), ICL=20<>37
cluster 5(N=73) has 4 sub-cluster at 5 (26), ICL=17<>37
cluster 3(N=134) has 2 sub-cluster at 2 (17), ICL=15<>37
cluster 1(N=789) has 4 sub-cluster at 4 (11), ICL=1.6<>37
cluster 7(N=15) has 2 sub-cluster at 2 (100), ICL=0.59<>37
cluster 1(N=789) has 4 sub-cluster at 4 (11), ICL=0<>37
Model Refinement takes 0.12 mins(max 1: 0.033)
Fit Model 4 of (6/10) K=7->8 N=2420
EM 8 takes 0 mins, 11 iterations
cluster 2(N=133) has 2 sub-cluster at 2 (10), ICL=62<>41
split 2 into 2 clusters
cluster 3(N=253) has 2 sub-cluster at 2 (10), ICL=53<>41
split 3 into 2 clusters
cluster 5(N=145) has 2 sub-cluster at 2 (11), ICL=19<>41
cluster 6(N=176) has 8 sub-cluster at 8 (45), ICL=17<>41
cluster 4(N=84) has 2 sub-cluster at 2 (20), ICL=15<>41
cluster 7(N=129) has 7 sub-cluster at 8 (49), ICL=8.8<>41
cluster 2(N=133) has 2 sub-cluster at 2 (10), ICL=0<>41
Model Refinement takes 0.23 mins(max 1: 0.083)
Fit Model 5 of (6/10) K=8->10 N=4841
EM 10 takes 0.017 mins, 11 iterations
cluster 2(N=100) has 2 sub-cluster at 2 (6), ICL=65<>45
split 2 into 2 clusters
cluster 4(N=30) has 2 sub-cluster at 2 (10), ICL=45<>45
split 4 into 2 clusters
cluster 7(N=300) has 5 sub-cluster at 5 (24), ICL=25<>45
cluster 6(N=190) has 3 sub-cluster at 3 (34), ICL=22<>45
cluster 5(N=465) has 8 sub-cluster at 8 (31), ICL=7.2<>45
cluster 8(N=310) has 6 sub-cluster at 7 (39), ICL=6.7<>45
cluster 3(N=156) has 6 sub-cluster at 8 (30), ICL=6.2<>45
cluster 9(N=357) has 8 sub-cluster at 8 (32), ICL=2.2<>45
cluster 2(N=100) has 2 sub-cluster at 2 (6), ICL=0<>45
Model Refinement takes 0.28 mins(max 1: 0.1)
Fit Model 6 of (6/10) K=10->12 N=9682
EM 12 takes 0 mins, 7 iterations
Warning in cell.TestSubCluster(x, as.matrix(y[cinc, ]), t, k, J = J, B = B, :
singularity in cluster 6
cluster 9(N=556) has 3 sub-cluster at 3 (11), ICL=66<>48
split 9 into 3 clusters
cluster 8(N=392) has 2 sub-cluster at 2 (13), ICL=41<>48
cluster 7(N=910) has 3 sub-cluster at 3 (8), ICL=32<>48
cluster 2(N=123) has 2 sub-cluster at 2 (8), ICL=30<>48
cluster 3(N=76) has 5 sub-cluster at 6 (63), ICL=13<>48
cluster 10(N=550) has 2 sub-cluster at 2 (15), ICL=12<>48
cluster 12(N=11) has 2 sub-cluster at 2 (100), ICL=1.9<>48
cluster 2(N=123) has 2 sub-cluster at 2 (8), ICL=0<>48
Model Refinement takes 0.33 mins(max 1: 0.1)
Fit Model 7 of (6/10) K=12->14 N=9682
EM 14 takes 0 mins, 5 iterations
Warning in cell.TestSubCluster(x, as.matrix(y[cinc, ]), t, k, J = J, B = B, :
singularity in cluster 6
cluster 7(N=900) has 2 sub-cluster at 2 (27), ICL=56<>48
split 7 into 2 clusters
cluster 14(N=11) has 2 sub-cluster at 2 (100), ICL=49<>48
split 14 into 2 clusters
cluster 8(N=391) has 2 sub-cluster at 2 (8), ICL=37<>48
cluster 2(N=123) has 2 sub-cluster at 2 (8), ICL=30<>48
cluster 11(N=87) has 2 sub-cluster at 2 (6), ICL=18<>48
cluster 10(N=178) has 5 sub-cluster at 7 (49), ICL=13<>48
cluster 12(N=515) has 2 sub-cluster at 2 (15), ICL=12<>48
cluster 9(N=362) has 6 sub-cluster at 7 (25), ICL=12<>48
cluster 4(N=308) has 2 sub-cluster at 2 (7), ICL=6.6<>48
cluster 3(N=75) has 3 sub-cluster at 4 (12), ICL=4.1<>48
cluster 2(N=123) has 2 sub-cluster at 2 (8), ICL=0<>48
Model Refinement takes 0.37 mins(max 1: 0.1)
Fit Model 8 of (6/10) K=14->16 N=9682
EM 14 takes 0.017 mins, 3 iterations
Warning in cell.TestSubCluster(x, as.matrix(y[cinc, ]), t, k, J = J, B = B, :
singularity in cluster 6
cluster 9(N=391) has 2 sub-cluster at 2 (8), ICL=37<>48
cluster 2(N=123) has 2 sub-cluster at 2 (8), ICL=30<>48
cluster 12(N=86) has 2 sub-cluster at 2 (6), ICL=18<>48
cluster 10(N=363) has 7 sub-cluster at 8 (47), ICL=14<>48
cluster 13(N=478) has 2 sub-cluster at 2 (14), ICL=14<>48
cluster 11(N=171) has 4 sub-cluster at 7 (40), ICL=10<>48
cluster 4(N=309) has 2 sub-cluster at 2 (10), ICL=7.5<>48
cluster 7(N=402) has 2 sub-cluster at 2 (16), ICL=6.3<>48
cluster 3(N=75) has 3 sub-cluster at 4 (12), ICL=4.1<>48
cluster 2(N=123) has 2 sub-cluster at 2 (8), ICL=0<>48
Model Refinement takes 0.4 mins(max 1: 0.1)
Fit Model 9 of (6/10) K=14->14 N=9682
EM 14 takes 0 mins, 3 iterations
Process completed at9
Major Iteration (Trans) (6/4) takes 1.9 mins
filtered from above:318
filtered from below:0
cluster 1(N=151) has 2 sub-cluster at 2 (16), ICL=165<>22
split 1 into 2 clusters
cluster 1(N=151) has 2 sub-cluster at 2 (16), ICL=0<>22
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, 9 iterations
cluster 1(N=92) has 3 sub-cluster at 3 (7), ICL=105<>25
split 1 into 3 clusters
cluster 2(N=211) has 2 sub-cluster at 2 (5), ICL=44<>25
split 2 into 2 clusters
cluster 1(N=92) has 3 sub-cluster at 3 (7), ICL=0<>25
Model Refinement takes 0.033 mins(max 2: 0.033)
Fit Model 2 of (6/10) K=2->5 N=605
EM 5 takes 0 mins, 9 iterations
cluster 1(N=76) has 2 sub-cluster at 2 (100), ICL=51<>28
split 1 into 2 clusters
cluster 5(N=66) has 2 sub-cluster at 2 (12), ICL=40<>28
split 5 into 2 clusters
cluster 2(N=24) has 2 sub-cluster at 2 (9), ICL=17<>28
cluster 3(N=61) has 2 sub-cluster at 2 (22), ICL=11<>28
cluster 4(N=386) has 8 sub-cluster at 8 (21), ICL=6.8<>28
cluster 1(N=76) has 2 sub-cluster at 2 (100), ICL=0<>28
Model Refinement takes 0.067 mins(max 4: 0.033)
Fit Model 3 of (6/10) K=5->7 N=1210
EM 6 takes 0 mins, 7 iterations
cluster 5(N=57) has 2 sub-cluster at 2 (6), ICL=31<>31
cluster 3(N=130) has 2 sub-cluster at 2 (11), ICL=28<>31
cluster 1(N=156) has 7 sub-cluster at 8 (48), ICL=23<>31
cluster 2(N=62) has 4 sub-cluster at 4 (21), ICL=22<>31
cluster 6(N=77) has 3 sub-cluster at 3 (17), ICL=20<>31
cluster 1(N=156) has 7 sub-cluster at 8 (48), ICL=0<>31
Model Refinement takes 0.1 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 5(N=109) has 3 sub-cluster at 3 (11), ICL=71<>34
split 5 into 3 clusters
cluster 3(N=229) has 2 sub-cluster at 2 (6), ICL=45<>34
split 3 into 2 clusters
cluster 1(N=285) has 5 sub-cluster at 5 (21), ICL=31<>34
cluster 6(N=140) has 2 sub-cluster at 2 (16), ICL=28<>34
cluster 2(N=101) has 4 sub-cluster at 4 (56), ICL=18<>34
cluster 1(N=285) has 5 sub-cluster at 5 (21), ICL=0<>34
Model Refinement takes 0.18 mins(max 4: 0.083)
Fit Model 5 of (6/10) K=6->9 N=4841
EM 9 takes 0 mins, 8 iterations
cluster 9(N=278) has 3 sub-cluster at 3 (9), ICL=37<>37
split 9 into 3 clusters
cluster 2(N=198) has 3 sub-cluster at 3 (9), ICL=27<>37
cluster 1(N=572) has 2 sub-cluster at 2 (8), ICL=27<>37
cluster 8(N=75) has 5 sub-cluster at 5 (27), ICL=26<>37
cluster 7(N=32) has 2 sub-cluster at 3 (27), ICL=17<>37
cluster 3(N=422) has 3 sub-cluster at 3 (23), ICL=16<>37
cluster 4(N=30) has 2 sub-cluster at 2 (12), ICL=16<>37
cluster 6(N=158) has 5 sub-cluster at 6 (22), ICL=12<>37
cluster 1(N=572) has 2 sub-cluster at 2 (8), ICL=0<>37
Model Refinement takes 0.25 mins(max 5: 0.1)
Fit Model 6 of (6/10) K=9->11 N=9682
EM 11 takes 0 mins, 7 iterations
cluster 8(N=156) has 4 sub-cluster at 4 (18), ICL=49<>40
split 8 into 4 clusters
cluster 2(N=391) has 2 sub-cluster at 2 (7), ICL=42<>40
split 2 into 2 clusters
cluster 4(N=60) has 2 sub-cluster at 2 (9), ICL=32<>40
cluster 3(N=903) has 3 sub-cluster at 3 (10), ICL=32<>40
cluster 1(N=1121) has 2 sub-cluster at 2 (12), ICL=29<>40
cluster 9(N=183) has 7 sub-cluster at 8 (61), ICL=22<>40
cluster 10(N=153) has 3 sub-cluster at 3 (7), ICL=19<>40
cluster 6(N=308) has 3 sub-cluster at 3 (33), ICL=12<>40
cluster 11(N=322) has 2 sub-cluster at 2 (8), ICL=12<>40
cluster 7(N=75) has 4 sub-cluster at 4 (15), ICL=8.8<>40
cluster 1(N=1121) has 2 sub-cluster at 2 (12), ICL=0<>40
Model Refinement takes 0.37 mins(max 5: 0.1)
Fit Model 7 of (6/10) K=11->15 N=9682
EM 15 takes 0.033 mins, 18 iterations
cluster 12(N=14) has 2 sub-cluster at 2 (100), ICL=50<>40
split 12 into 2 clusters
cluster 4(N=906) has 3 sub-cluster at 3 (17), ICL=42<>40
split 4 into 3 clusters
cluster 5(N=60) has 2 sub-cluster at 2 (9), ICL=31<>40
cluster 14(N=164) has 2 sub-cluster at 2 (20), ICL=24<>40
cluster 9(N=95) has 4 sub-cluster at 4 (19), ICL=21<>40
cluster 13(N=168) has 5 sub-cluster at 6 (30), ICL=21<>40
cluster 10(N=13) has 2 sub-cluster at 2 (100), ICL=18<>40
cluster 11(N=284) has 3 sub-cluster at 4 (30), ICL=18<>40
cluster 3(N=196) has 3 sub-cluster at 3 (16), ICL=16<>40
cluster 2(N=250) has 6 sub-cluster at 7 (60), ICL=14<>40
cluster 15(N=319) has 6 sub-cluster at 6 (33), ICL=13<>40
cluster 7(N=309) has 2 sub-cluster at 2 (8), ICL=9.5<>40
cluster 8(N=75) has 3 sub-cluster at 4 (10), ICL=6.6<>40
cluster 2(N=250) has 6 sub-cluster at 7 (60), ICL=0<>40
Model Refinement takes 0.38 mins(max 6: 0.1)
Fit Model 8 of (6/10) K=15->18 N=9682
EM 18 takes 0 mins, 6 iterations
cluster 15(N=8) has 2 sub-cluster at 2 (100), ICL=42<>40
split 15 into 2 clusters
cluster 11(N=94) has 5 sub-cluster at 6 (23), ICL=36<>40
cluster 7(N=60) has 2 sub-cluster at 2 (10), ICL=33<>40
cluster 13(N=344) has 2 sub-cluster at 2 (19), ICL=25<>40
cluster 17(N=160) has 2 sub-cluster at 2 (17), ICL=24<>40
cluster 12(N=13) has 2 sub-cluster at 2 (100), ICL=18<>40
cluster 16(N=167) has 5 sub-cluster at 6 (41), ICL=17<>40
cluster 18(N=316) has 8 sub-cluster at 8 (32), ICL=16<>40
cluster 3(N=197) has 6 sub-cluster at 8 (33), ICL=16<>40
cluster 2(N=250) has 7 sub-cluster at 8 (53), ICL=16<>40
cluster 4(N=337) has 3 sub-cluster at 4 (37), ICL=14<>40
cluster 9(N=308) has 2 sub-cluster at 2 (10), ICL=11<>40
cluster 5(N=412) has 6 sub-cluster at 6 (46), ICL=6<>40
cluster 6(N=396) has 6 sub-cluster at 6 (25), ICL=1.5<>40
cluster 2(N=250) has 7 sub-cluster at 8 (53), ICL=0<>40
Model Refinement takes 0.43 mins(max 8: 0.083)
Fit Model 9 of (6/10) K=18->19 N=9682
EM 18 takes 0.017 mins, 3 iterations
cluster 7(N=61) has 2 sub-cluster at 2 (9), ICL=33<>40
cluster 17(N=162) has 3 sub-cluster at 3 (10), ICL=21<>40
cluster 13(N=356) has 2 sub-cluster at 2 (6), ICL=19<>40
cluster 12(N=13) has 2 sub-cluster at 2 (100), ICL=18<>40
cluster 11(N=94) has 4 sub-cluster at 4 (22), ICL=16<>40
cluster 10(N=74) has 3 sub-cluster at 4 (38), ICL=16<>40
cluster 3(N=197) has 6 sub-cluster at 7 (29), ICL=16<>40
cluster 16(N=167) has 6 sub-cluster at 8 (43), ICL=13<>40
cluster 18(N=314) has 2 sub-cluster at 2 (6), ICL=13<>40
cluster 2(N=250) has 7 sub-cluster at 8 (35), ICL=11<>40
cluster 9(N=308) has 8 sub-cluster at 8 (28), ICL=7.1<>40
cluster 4(N=336) has 7 sub-cluster at 8 (25), ICL=0.63<>40
cluster 5(N=407) has 7 sub-cluster at 7 (30), ICL=0.27<>40
cluster 2(N=250) has 7 sub-cluster at 8 (35), ICL=0<>40
Model Refinement takes 0.42 mins(max 8: 0.083)
Fit Model 10 of (6/10) K=18->18 N=9682
EM 18 takes 0.017 mins, 7 iterations
Process completed at10
Major Iteration (Trans) (6/4) takes 2.4 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