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This page was generated on 2023-05-26 06:18:16 -0000 (Fri, 26 May 2023).

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kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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BUILD results for SemDist on kunpeng2


To the developers/maintainers of the SemDist package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SemDist.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1848/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SemDist 1.35.0  (landing page)
Ian Gonzalez
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/SemDist
git_branch: devel
git_last_commit: 662bc15
git_last_commit_date: 2023-04-25 14:33:53 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

Summary

Package: SemDist
Version: 1.35.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data SemDist
StartedAt: 2023-05-26 01:44:32 -0000 (Fri, 26 May 2023)
EndedAt: 2023-05-26 01:45:13 -0000 (Fri, 26 May 2023)
EllapsedTime: 41.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data SemDist
###
##############################################################################
##############################################################################


* 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