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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GWASTools
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* checking for file ‘GWASTools/DESCRIPTION’ ... OK
* preparing ‘GWASTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Affymetrix.Rmd’ using rmarkdown
Error: processing vignette 'Affymetrix.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘Affymetrix.Rmd’
--- re-building ‘DataCleaning.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
adding variables: genotype
adding variables: quality, X, Y
adding variables: BAlleleFreq, LogRRatio
Thu May 7 16:02:24 2026 Load genotype dataset ...
Thu May 7 16:02:24 2026 1/3 A
Thu May 7 16:02:24 2026 2/3 B
Thu May 7 16:02:24 2026 3/3 C
Loading required package: gdsfmt
All row numbers refer to row in the full pedigree (not just within family).
Correct current problems and rerun pedigreeCheck.
There may be additional problems not investigated because of the current problems.
All row numbers refer to row in the full pedigree (not just within family).
Correct current problems and rerun pedigreeCheck.
There may be additional problems not investigated because of the current problems.
All row numbers refer to row in the full pedigree (not just within family).
Correct current problems and rerun pedigreeCheck.
There may be additional problems not investigated because of the current problems.
subject 1 out of 34, 2 replications
subject 2 out of 34, 2 replications
subject 3 out of 34, 2 replications
subject 4 out of 34, 2 replications
subject 5 out of 34, 2 replications
subject 6 out of 34, 2 replications
subject 7 out of 34, 2 replications
subject 8 out of 34, 2 replications
subject 9 out of 34, 2 replications
subject 10 out of 34, 2 replications
subject 11 out of 34, 2 replications
subject 12 out of 34, 2 replications
subject 13 out of 34, 2 replications
subject 14 out of 34, 2 replications
subject 15 out of 34, 2 replications
subject 16 out of 34, 2 replications
subject 17 out of 34, 2 replications
subject 18 out of 34, 2 replications
subject 19 out of 34, 2 replications
subject 20 out of 34, 2 replications
subject 21 out of 34, 2 replications
subject 22 out of 34, 2 replications
subject 23 out of 34, 2 replications
subject 24 out of 34, 2 replications
subject 25 out of 34, 2 replications
subject 26 out of 34, 2 replications
subject 27 out of 34, 2 replications
subject 28 out of 34, 2 replications
subject 29 out of 34, 2 replications
subject 30 out of 34, 2 replications
subject 31 out of 34, 2 replications
subject 32 out of 34, 2 replications
subject 33 out of 34, 2 replications
subject 34 out of 34, 2 replications
Preparing data structures...
Thu May 7 16:02:26 2026 [ 1 ] family: 4, child: 200047857, 1
Thu May 7 16:02:26 2026 [ 2 ] family: 4, child: 200047857, 2
Thu May 7 16:02:26 2026 [ 3 ] family: 4, child: 200047857, 3
Thu May 7 16:02:26 2026 [ 4 ] family: 4, child: 200047857, 4
Thu May 7 16:02:26 2026 [ 5 ] family: 5, child: 200102386, 1
Thu May 7 16:02:26 2026 [ 6 ] family: 5, child: 200102386, 2
Thu May 7 16:02:26 2026 [ 7 ] family: 5, child: 200102386, 3
Thu May 7 16:02:26 2026 [ 8 ] family: 5, child: 200102386, 4
Thu May 7 16:02:26 2026 [ 9 ] family: 5, child: 200102386, 5
Thu May 7 16:02:26 2026 [ 10 ] family: 5, child: 200102386, 6
Thu May 7 16:02:26 2026 [ 11 ] family: 5, child: 200102386, 7
Thu May 7 16:02:26 2026 [ 12 ] family: 5, child: 200102386, 8
Thu May 7 16:02:26 2026 [ 13 ] family: 9, child: 200066330, 1
Thu May 7 16:02:26 2026 [ 14 ] family: 9, child: 200066330, 2
Thu May 7 16:02:26 2026 [ 15 ] family: 9, child: 200066330, 3
Thu May 7 16:02:26 2026 [ 16 ] family: 9, child: 200066330, 4
Thu May 7 16:02:26 2026 [ 17 ] family: 12, child: 200013233, 1
Thu May 7 16:02:26 2026 [ 18 ] family: 12, child: 200013233, 2
Thu May 7 16:02:26 2026 [ 19 ] family: 12, child: 200013233, 3
Thu May 7 16:02:26 2026 [ 20 ] family: 12, child: 200013233, 4
Thu May 7 16:02:26 2026 [ 21 ] family: 28, child: 200034659, 1
Thu May 7 16:02:26 2026 [ 22 ] family: 28, child: 200034659, 2
Thu May 7 16:02:26 2026 [ 23 ] family: 28, child: 200034659, 3
Thu May 7 16:02:26 2026 [ 24 ] family: 28, child: 200034659, 4
Thu May 7 16:02:26 2026 [ 25 ] family: 1334, child: 200016815, 1
Thu May 7 16:02:26 2026 [ 26 ] family: 1334, child: 200016815, 2
Thu May 7 16:02:26 2026 [ 27 ] family: 1334, child: 200016815, 3
Thu May 7 16:02:26 2026 [ 28 ] family: 1334, child: 200016815, 4
Thu May 7 16:02:26 2026 [ 29 ] family: 1334, child: 200016815, 5
Thu May 7 16:02:26 2026 [ 30 ] family: 1334, child: 200016815, 6
Thu May 7 16:02:26 2026 [ 31 ] family: 1334, child: 200016815, 7
Thu May 7 16:02:26 2026 [ 32 ] family: 1334, child: 200016815, 8
Thu May 7 16:02:26 2026 [ 33 ] family: 1340, child: 200076256, 1
Thu May 7 16:02:26 2026 [ 34 ] family: 1340, child: 200076256, 2
Thu May 7 16:02:26 2026 [ 35 ] family: 1340, child: 200076256, 3
Thu May 7 16:02:26 2026 [ 36 ] family: 1340, child: 200076256, 4
Thu May 7 16:02:26 2026 [ 37 ] family: 1341, child: 200015835, 1
Thu May 7 16:02:26 2026 [ 38 ] family: 1341, child: 200015835, 2
Thu May 7 16:02:26 2026 [ 39 ] family: 1341, child: 200030290, 1
Thu May 7 16:02:26 2026 [ 40 ] family: 1341, child: 200030290, 2
Thu May 7 16:02:26 2026 [ 41 ] family: 1341, child: 200030290, 3
Thu May 7 16:02:26 2026 [ 42 ] family: 1341, child: 200030290, 4
Thu May 7 16:02:26 2026 [ 43 ] family: 1341, child: 200030290, 5
Thu May 7 16:02:26 2026 [ 44 ] family: 1341, child: 200030290, 6
Thu May 7 16:02:26 2026 [ 45 ] family: 1341, child: 200030290, 7
Thu May 7 16:02:26 2026 [ 46 ] family: 1341, child: 200030290, 8
Thu May 7 16:02:26 2026 [ 47 ] family: 1344, child: 200071490, 1
Thu May 7 16:02:26 2026 [ 48 ] family: 1344, child: 200071490, 2
Thu May 7 16:02:26 2026 [ 49 ] family: 1344, child: 200071490, 3
Thu May 7 16:02:26 2026 [ 50 ] family: 1344, child: 200071490, 4
Thu May 7 16:02:26 2026 [ 51 ] family: 1344, child: 200071490, 5
Thu May 7 16:02:26 2026 [ 52 ] family: 1344, child: 200071490, 6
Thu May 7 16:02:26 2026 [ 53 ] family: 1344, child: 200071490, 7
Thu May 7 16:02:26 2026 [ 54 ] family: 1344, child: 200071490, 8
Thu May 7 16:02:26 2026 [ 55 ] family: 1347, child: 200121301, 1
Thu May 7 16:02:26 2026 [ 56 ] family: 1347, child: 200121301, 2
Thu May 7 16:02:26 2026 [ 57 ] family: 1347, child: 200121301, 3
Thu May 7 16:02:26 2026 [ 58 ] family: 1347, child: 200121301, 4
Thu May 7 16:02:26 2026 [ 59 ] family: 1347, child: 200121301, 5
Thu May 7 16:02:26 2026 [ 60 ] family: 1347, child: 200121301, 6
Thu May 7 16:02:26 2026 [ 61 ] family: 1347, child: 200121301, 7
Thu May 7 16:02:27 2026 [ 62 ] family: 1347, child: 200121301, 8
Thu May 7 16:02:27 2026 [ 63 ] family: 1362, child: 200003297, 1
Thu May 7 16:02:27 2026 [ 64 ] family: 1362, child: 200003297, 2
Thu May 7 16:02:27 2026 [ 65 ] family: 1362, child: 200003297, 3
Thu May 7 16:02:27 2026 [ 66 ] family: 1362, child: 200003297, 4
Thu May 7 16:02:27 2026 [ 67 ] family: 1362, child: 200024383, 1
Thu May 7 16:02:27 2026 [ 68 ] family: 1362, child: 200024383, 2
Thu May 7 16:02:27 2026 [ 69 ] family: 1362, child: 200024383, 3
Thu May 7 16:02:27 2026 [ 70 ] family: 1362, child: 200024383, 4
Thu May 7 16:02:27 2026 [ 71 ] family: 1362, child: 200024383, 5
Thu May 7 16:02:27 2026 [ 72 ] family: 1362, child: 200024383, 6
Thu May 7 16:02:27 2026 [ 73 ] family: 1362, child: 200024383, 7
Thu May 7 16:02:27 2026 [ 74 ] family: 1362, child: 200024383, 8
Thu May 7 16:02:27 2026 [ 75 ] family: 1408, child: 200074814, 1
Thu May 7 16:02:27 2026 [ 76 ] family: 1408, child: 200074814, 2
Thu May 7 16:02:27 2026 [ 77 ] family: 1408, child: 200074814, 3
Thu May 7 16:02:27 2026 [ 78 ] family: 1408, child: 200074814, 4
Thu May 7 16:02:27 2026 [ 79 ] family: 1408, child: 200074814, 5
Thu May 7 16:02:27 2026 [ 80 ] family: 1408, child: 200074814, 6
Thu May 7 16:02:27 2026 [ 81 ] family: 1408, child: 200074814, 7
Thu May 7 16:02:27 2026 [ 82 ] family: 1408, child: 200074814, 8
Averaging over duplicate trios...
start time = 2026-05-07 16:02:27.122055
plot number = 1 system time = 2026-05-07 16:02:27.123467
plot number = 2 system time = 2026-05-07 16:02:27.13287
plot number = 3 system time = 2026-05-07 16:02:27.142358
plot number = 4 system time = 2026-05-07 16:02:27.151446
plot number = 5 system time = 2026-05-07 16:02:27.160487
plot number = 6 system time = 2026-05-07 16:02:27.169663
plot number = 7 system time = 2026-05-07 16:02:27.178847
plot number = 8 system time = 2026-05-07 16:02:27.188121
plot number = 9 system time = 2026-05-07 16:02:27.197494
Beginning Calculations...
Block 1 of 1 Completed - 0.001259 secs
Beginning Calculations...
Block 1 of 1 Completed - 0.000658 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.03381 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.03782 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.03053 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.007467 secs
Reading in Phenotype and Covariate Data...
Running analysis with 24 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.001976 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.006772 secs
start time = 2026-05-07 16:02:27.685873
plot number = 1 system time = 2026-05-07 16:02:27.686637
plot number = 2 system time = 2026-05-07 16:02:27.695973
plot number = 3 system time = 2026-05-07 16:02:27.704466
plot number = 4 system time = 2026-05-07 16:02:27.713063
plot number = 5 system time = 2026-05-07 16:02:27.721378
plot number = 6 system time = 2026-05-07 16:02:27.729693
plot number = 7 system time = 2026-05-07 16:02:27.738053
plot number = 8 system time = 2026-05-07 16:02:27.746315
plot number = 9 system time = 2026-05-07 16:02:27.754728
--- finished re-building ‘DataCleaning.Rnw’
--- re-building ‘Formats.Rnw’ using Sweave
--- finished re-building ‘Formats.Rnw’
SUMMARY: processing the following file failed:
‘Affymetrix.Rmd’
Error: Vignette re-building failed.
Execution halted
