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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings groHMM_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/groHMM.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘groHMM/DESCRIPTION’ ... OK
* this is package ‘groHMM’ version ‘1.33.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'MASS', 'parallel', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'GenomicAlignments', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘groHMM’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives no person with maintainer role, valid email
address and non-empty name.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘groHMM.Rnw’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘groHMM.Rnw’
  ...

> kgdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

> library(GenomicFeatures)

> kgChr7 <- transcripts(kgdb, filter = list(tx_chrom = "chr7"), 
+     columns = c("gene_id", "tx_id", "tx_name"))
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘groHMM.Rnw’ using Sweave
Loading required package: MASS
Loading required package: parallel
Loading required package: S4Vectors
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


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi

Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:MASS’:

    select

Warning in makeConsensusAnnotations(kgChr7, keytype = "gene_id", mc.cores = getOption("mc.cores")) :
  562 ranges do not have gene_id and they are 
            dropped
Reduce isoforms(701) ... Killed

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/groHMM.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL groHMM
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:43:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c Windowing.c -o Windowing.o
Windowing.c: In function ‘WindowAnalysis’:
Windowing.c:146:13: warning: unused variable ‘II’ [-Wunused-variable]
  146 |         int II = 0;
      |             ^~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmEM.c:50:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c hmmFwBw.c -o hmmFwBw.o
hmmFwBw.c: In function ‘forward’:
hmmFwBw.c:142:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  142 |       for(k=1; k<n; k++)
      |       ^~~
hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  145 |         for (k = 0; k<n; k++) {
      |         ^~~
In file included from hmmFwBw.c:45:
At top level:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmFwBw.c:45:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function ‘SStatsNormExp’:
hmmMiscFunctions.c:384:10: warning: unused variable ‘wi’ [-Wunused-variable]
  384 |   double wi, *newEx;
      |          ^~
hmmMiscFunctions.c: In function ‘UpdateNormExp’:
hmmMiscFunctions.c:417:10: warning: unused variable ‘epsilon’ [-Wunused-variable]
  417 |   double epsilon=0.00001;
      |          ^~~~~~~
In file included from hmmHeader.h:36,
                 from hmmMiscFunctions.c:43:
At top level:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:48:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmViterbi.c:48:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-groHMM/00new/groHMM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (groHMM)