This page was generated on 2023-05-26 06:18:16 -0000 (Fri, 26 May 2023).
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data SemDist
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* checking for file ‘SemDist/DESCRIPTION’ ... OK
* preparing ‘SemDist’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘introduction.rnw’ using Sweave
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: GO.db
Loading required package: annotate
Loading required package: XML
Getting true IAs
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
Calculating RU, MI
Getting true IAs
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
Calculating RU, MI
Working on data for file: /tmp/Rtmp4m8I7l/Rinst158aff1014f10/SemDist/extdata/MFO_PREDS_TEST.txt
Getting true terms
Getting true IAs
Now working on threshold: 0.95
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 10.0537744342887, MI: 1.24450581070304
Now working on threshold: 0.9
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 9.43488433943007, MI: 1.90438819980418
Now working on threshold: 0.85
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 8.87230607236529, MI: 2.43042794675168
Now working on threshold: 0.8
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 8.47489605506715, MI: 3.22678524999358
Now working on threshold: 0.75
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 8.22335297346735, MI: 3.96628348443481
Now working on threshold: 0.7
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 7.71961299047681, MI: 4.85629255591759
Now working on threshold: 0.65
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 7.2200044238661, MI: 6.0098180845365
Now working on threshold: 0.6
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 6.84314834777473, MI: 7.47794158858785
Now working on threshold: 0.55
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 6.28555707245137, MI: 10.1515907153763
Now working on threshold: 0.5
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 5.61598381150819, MI: 15.0450912028459
Now working on threshold: 0.45
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 5.00711519147839, MI: 22.3539915496098
Now working on threshold: 0.4
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 4.31210874430507, MI: 36.670308442448
Now working on threshold: 0.35
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 3.63802606810064, MI: 56.7762339186203
Now working on threshold: 0.3
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 2.90873607104053, MI: 90.9779318548042
Now working on threshold: 0.25
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 2.27714481009132, MI: 124.574015216105
Now working on threshold: 0.2
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 2.09678013814739, MI: 137.855149226555
Now working on threshold: 0.15
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 2.0862687770842, MI: 138.345526472614
Now working on threshold: 0.0999999999999999
Getting sequence predicted terms.
Now working on threshold: 0.05
Getting sequence predicted terms.
Working on data for file: /tmp/Rtmp4m8I7l/Rinst158aff1014f10/SemDist/extdata/MFO_PREDS_TEST.txt
Getting true terms
Getting true IAs
Now working on threshold: 0.95
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 10.0537744342887, MI: 1.24450581070304
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.9
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 9.43488433943007, MI: 1.90438819980418
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.85
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 8.87230607236529, MI: 2.43042794675168
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.8
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 8.47489605506715, MI: 3.22678524999358
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.75
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 8.22335297346735, MI: 3.96628348443481
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.7
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 7.71961299047681, MI: 4.85629255591759
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.65
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 7.2200044238661, MI: 6.0098180845365
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.6
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 6.84314834777473, MI: 7.47794158858785
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.55
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 6.28555707245137, MI: 10.1515907153763
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.5
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 5.61598381150819, MI: 15.0450912028459
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.45
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 5.00711519147839, MI: 22.3539915496098
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.4
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 4.31210874430507, MI: 36.670308442448
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.35
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 3.63802606810064, MI: 56.7762339186203
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.3
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 2.90873607104053, MI: 90.9779318548042
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.25
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 2.27714481009132, MI: 124.574015216105
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.2
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 2.09678013814739, MI: 137.855149226555
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.15
Getting sequence predicted terms.
Getting IA values for predicted terms.
Doing the same for the intersect.
RU: 2.0862687770842, MI: 138.345526472614
Warning in answers$Wprecision[answers$threshold == thresh] <- Wprecision :
number of items to replace is not a multiple of replacement length
Now working on threshold: 0.0999999999999999
Getting sequence predicted terms.
Now working on threshold: 0.05
Getting sequence predicted terms.
Error: processing vignette 'introduction.rnw' failed with diagnostics:
unable to run pdflatex on 'introduction.tex'
LaTeX errors:
! LaTeX Error: File `cleveref.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.7 \usepackage
{natbib}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘introduction.rnw’
SUMMARY: processing the following file failed:
‘introduction.rnw’
Error: Vignette re-building failed.
Execution halted