############################################################################## ############################################################################## ### ### 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 (15), ICL=151<>26 split 1 into 2 clusters cluster 1(N=151) has 2 sub-cluster at 2 (15), ICL=0<>26 Model Refinement takes 0.05 mins(max 1: 0.05) Fit Model 1 of (6/10) K=1->2 N=302 EM 2 takes 0 mins, 8 iterations cluster 2(N=80) has 2 sub-cluster at 2 (8), ICL=121<>30 split 2 into 2 clusters cluster 1(N=225) has 2 sub-cluster at 2 (8), ICL=21<>30 cluster 1(N=225) has 2 sub-cluster at 2 (8), ICL=0<>30 Model Refinement takes 0.05 mins(max 1: 0.033) Fit Model 2 of (6/10) K=2->3 N=605 EM 3 takes 0 mins, 6 iterations cluster 1(N=435) has 2 sub-cluster at 2 (16), ICL=72<>34 split 1 into 2 clusters cluster 2(N=100) has 2 sub-cluster at 2 (8), ICL=54<>34 split 2 into 2 clusters cluster 3(N=72) has 2 sub-cluster at 2 (7), ICL=20<>34 cluster 1(N=435) has 2 sub-cluster at 2 (16), ICL=0<>34 Model Refinement takes 0.067 mins(max 1: 0.033) Fit Model 3 of (6/10) K=3->5 N=1210 EM 5 takes 0 mins, 11 iterations cluster 2(N=134) has 2 sub-cluster at 2 (7), ICL=94<>37 split 2 into 2 clusters cluster 5(N=110) has 2 sub-cluster at 2 (11), ICL=27<>37 cluster 3(N=130) has 2 sub-cluster at 2 (8), ICL=20<>37 cluster 4(N=55) has 2 sub-cluster at 2 (11), ICL=6.2<>37 cluster 2(N=134) has 2 sub-cluster at 2 (7), ICL=0<>37 Model Refinement takes 0.083 mins(max 2: 0.033) Fit Model 4 of (6/10) K=5->6 N=2420 EM 6 takes 0 mins, 6 iterations cluster 2(N=118) has 2 sub-cluster at 2 (9), ICL=55<>41 split 2 into 2 clusters cluster 4(N=289) has 2 sub-cluster at 2 (7), ICL=28<>41 cluster 6(N=220) has 3 sub-cluster at 3 (33), ICL=25<>41 cluster 5(N=95) has 5 sub-cluster at 6 (31), ICL=21<>41 cluster 3(N=153) has 8 sub-cluster at 8 (21), ICL=18<>41 cluster 2(N=118) has 2 sub-cluster at 2 (9), ICL=0<>41 Model Refinement takes 0.13 mins(max 1: 0.05) Fit Model 5 of (6/10) K=6->7 N=4841 EM 7 takes 0 mins, 6 iterations cluster 7(N=479) has 2 sub-cluster at 2 (5), ICL=108<>45 split 7 into 2 clusters cluster 3(N=116) has 2 sub-cluster at 2 (6), ICL=68<>45 split 3 into 2 clusters cluster 2(N=167) has 2 sub-cluster at 2 (67), ICL=56<>45 split 2 into 2 clusters cluster 5(N=561) has 2 sub-cluster at 2 (7), ICL=41<>45 cluster 4(N=265) has 5 sub-cluster at 5 (27), ICL=28<>45 cluster 6(N=186) has 3 sub-cluster at 3 (8), ICL=18<>45 cluster 2(N=167) has 2 sub-cluster at 2 (67), ICL=0<>45 Model Refinement takes 0.17 mins(max 1: 0.05) Fit Model 6 of (6/10) K=7->10 N=9682 EM 9 takes 0.017 mins, 8 iterations cluster 5(N=557) has 3 sub-cluster at 3 (11), ICL=65<>48 split 5 into 3 clusters cluster 6(N=1121) has 2 sub-cluster at 2 (9), ICL=49<>48 split 6 into 2 clusters cluster 3(N=153) has 4 sub-cluster at 4 (17), ICL=42<>48 cluster 7(N=392) has 3 sub-cluster at 3 (34), ICL=38<>48 cluster 9(N=60) has 2 sub-cluster at 2 (9), ICL=30<>48 cluster 8(N=908) has 3 sub-cluster at 3 (12), ICL=29<>48 cluster 4(N=76) has 5 sub-cluster at 6 (94), ICL=13<>48 cluster 2(N=314) has 2 sub-cluster at 2 (9), ICL=7.4<>48 cluster 2(N=314) has 2 sub-cluster at 2 (9), ICL=0<>48 Model Refinement takes 0.23 mins(max 1: 0.067) Fit Model 7 of (6/10) K=9->12 N=9682 EM 12 takes 0.017 mins, 7 iterations cluster 10(N=391) has 2 sub-cluster at 2 (8), ICL=37<>48 cluster 12(N=60) has 2 sub-cluster at 2 (9), ICL=30<>48 cluster 11(N=898) has 3 sub-cluster at 3 (9), ICL=29<>48 cluster 3(N=122) has 3 sub-cluster at 3 (28), ICL=26<>48 cluster 9(N=425) has 2 sub-cluster at 2 (6), ICL=19<>48 cluster 7(N=88) has 2 sub-cluster at 2 (7), ICL=18<>48 cluster 5(N=362) has 2 sub-cluster at 2 (7), ICL=12<>48 cluster 6(N=173) has 4 sub-cluster at 5 (21), ICL=11<>48 cluster 2(N=309) has 2 sub-cluster at 2 (10), ICL=7.5<>48 cluster 4(N=75) has 3 sub-cluster at 4 (12), ICL=4.1<>48 cluster 2(N=309) has 2 sub-cluster at 2 (10), ICL=0<>48 Model Refinement takes 0.27 mins(max 1: 0.067) Fit Model 8 of (6/10) K=12->12 N=9682 EM 12 takes 0 mins, 3 iterations Process completed at8 Major Iteration (Trans) (6/4) takes 1.1 mins filtered from above:318 filtered from below:0 cluster 1(N=151) has 2 sub-cluster at 2 (9), ICL=168<>22 split 1 into 2 clusters cluster 1(N=151) has 2 sub-cluster at 2 (9), ICL=0<>22 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=77) has 3 sub-cluster at 3 (9), ICL=98<>25 split 2 into 3 clusters cluster 1(N=225) has 2 sub-cluster at 2 (7), ICL=37<>25 split 1 into 2 clusters cluster 1(N=225) has 2 sub-cluster at 2 (7), ICL=0<>25 Model Refinement takes 0.017 mins(max 1: 0.017) Fit Model 2 of (6/10) K=2->5 N=605 EM 5 takes 0 mins, 10 iterations cluster 2(N=78) has 2 sub-cluster at 2 (13), ICL=45<>28 split 2 into 2 clusters cluster 5(N=63) has 5 sub-cluster at 6 (56), ICL=21<>28 cluster 3(N=55) has 2 sub-cluster at 2 (8), ICL=13<>28 cluster 4(N=30) has 3 sub-cluster at 3 (6), ICL=4.4<>28 cluster 2(N=78) has 2 sub-cluster at 2 (13), ICL=0<>28 Model Refinement takes 0.033 mins(max 2: 0.017) Fit Model 3 of (6/10) K=5->6 N=1210 EM 6 takes 0.017 mins, 11 iterations cluster 4(N=103) has 2 sub-cluster at 2 (5), ICL=38<>31 split 4 into 2 clusters cluster 2(N=60) has 2 sub-cluster at 2 (6), ICL=33<>31 split 2 into 2 clusters cluster 6(N=148) has 4 sub-cluster at 5 (26), ICL=19<>31 cluster 5(N=47) has 2 sub-cluster at 2 (100), ICL=18<>31 cluster 3(N=72) has 2 sub-cluster at 2 (84), ICL=2.6<>31 cluster 2(N=60) has 2 sub-cluster at 2 (6), ICL=0<>31 Model Refinement takes 0.067 mins(max 1: 0.017) Fit Model 4 of (6/10) K=6->8 N=2420 EM 8 takes 0 mins, 9 iterations cluster 2(N=43) has 2 sub-cluster at 2 (8), ICL=32<>34 cluster 8(N=266) has 2 sub-cluster at 2 (12), ICL=29<>34 cluster 4(N=150) has 2 sub-cluster at 2 (8), ICL=21<>34 cluster 7(N=95) has 3 sub-cluster at 3 (20), ICL=20<>34 cluster 5(N=228) has 2 sub-cluster at 2 (13), ICL=19<>34 cluster 3(N=76) has 4 sub-cluster at 5 (21), ICL=17<>34 cluster 6(N=17) has 2 sub-cluster at 2 (100), ICL=4<>34 cluster 2(N=43) has 2 sub-cluster at 2 (8), ICL=0<>34 Model Refinement takes 0.13 mins(max 1: 0.05) Fit Model 5 of (6/10) K=8->8 N=4841 EM 8 takes 0 mins, 6 iterations cluster 2(N=99) has 2 sub-cluster at 2 (6), ICL=64<>37 split 2 into 2 clusters cluster 8(N=593) has 2 sub-cluster at 2 (7), ICL=38<>37 split 8 into 2 clusters cluster 4(N=262) has 3 sub-cluster at 3 (18), ICL=35<>37 cluster 7(N=187) has 7 sub-cluster at 7 (50), ICL=25<>37 cluster 3(N=135) has 6 sub-cluster at 6 (21), ICL=9.3<>37 cluster 5(N=465) has 8 sub-cluster at 8 (28), ICL=8.5<>37 cluster 2(N=99) has 2 sub-cluster at 2 (6), ICL=0<>37 Model Refinement takes 0.17 mins(max 1: 0.067) Fit Model 6 of (6/10) K=8->10 N=9682 EM 10 takes 0 mins, 6 iterations cluster 5(N=557) has 3 sub-cluster at 3 (11), ICL=69<>40 split 5 into 3 clusters cluster 8(N=392) has 2 sub-cluster at 2 (13), ICL=43<>40 split 8 into 2 clusters cluster 7(N=60) has 2 sub-cluster at 2 (9), ICL=32<>40 cluster 3(N=122) has 3 sub-cluster at 3 (28), ICL=29<>40 cluster 6(N=909) has 4 sub-cluster at 4 (15), ICL=27<>40 cluster 10(N=380) has 2 sub-cluster at 3 (13), ICL=19<>40 cluster 2(N=76) has 4 sub-cluster at 5 (15), ICL=14<>40 cluster 4(N=314) has 2 sub-cluster at 2 (6), ICL=7.9<>40 cluster 2(N=76) has 4 sub-cluster at 5 (15), ICL=0<>40 Model Refinement takes 0.25 mins(max 1: 0.067) Fit Model 7 of (6/10) K=10->13 N=9682 EM 13 takes 0.017 mins, 4 iterations cluster 8(N=898) has 2 sub-cluster at 2 (34), ICL=57<>40 split 8 into 2 clusters cluster 3(N=123) has 2 sub-cluster at 2 (9), ICL=32<>40 cluster 9(N=60) has 2 sub-cluster at 2 (9), ICL=31<>40 cluster 10(N=221) has 6 sub-cluster at 7 (98), ICL=23<>40 cluster 7(N=87) has 3 sub-cluster at 3 (10), ICL=20<>40 cluster 13(N=389) has 2 sub-cluster at 2 (10), ICL=18<>40 cluster 5(N=363) has 7 sub-cluster at 7 (30), ICL=16<>40 cluster 11(N=217) has 7 sub-cluster at 8 (20), ICL=12<>40 cluster 6(N=181) has 6 sub-cluster at 8 (26), ICL=11<>40 cluster 4(N=307) has 2 sub-cluster at 2 (7), ICL=9<>40 cluster 2(N=75) has 3 sub-cluster at 4 (10), ICL=6.6<>40 cluster 2(N=75) has 3 sub-cluster at 4 (10), ICL=0<>40 Model Refinement takes 0.28 mins(max 1: 0.067) Fit Model 8 of (6/10) K=13->14 N=9682 EM 14 takes 0.017 mins, 3 iterations cluster 10(N=61) has 2 sub-cluster at 2 (9), ICL=33<>40 cluster 3(N=123) has 2 sub-cluster at 2 (9), ICL=32<>40 cluster 14(N=395) has 3 sub-cluster at 4 (34), ICL=25<>40 cluster 7(N=86) has 5 sub-cluster at 5 (26), ICL=20<>40 cluster 11(N=221) has 6 sub-cluster at 8 (49), ICL=17<>40 cluster 5(N=363) has 8 sub-cluster at 8 (28), ICL=17<>40 cluster 6(N=173) has 4 sub-cluster at 5 (18), ICL=14<>40 cluster 12(N=220) has 6 sub-cluster at 7 (38), ICL=13<>40 cluster 4(N=308) has 2 sub-cluster at 2 (7), ICL=9.1<>40 cluster 2(N=75) has 3 sub-cluster at 4 (10), ICL=6.6<>40 cluster 8(N=399) has 6 sub-cluster at 7 (42), ICL=1.2<>40 cluster 2(N=75) has 3 sub-cluster at 4 (10), ICL=0<>40 Model Refinement takes 0.3 mins(max 1: 0.067) Fit Model 9 of (6/10) K=14->14 N=9682 EM 14 takes 0.017 mins, 3 iterations Process completed at9 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 to proceed, or enter new name. (Default extension: sty) ! Emergency stop. 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