R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
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, 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: 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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum, scale, sweep

Loading required package: rhdf5

Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls

[1] TRUE
> setAutoRealizationBackend("HDF5Array")
> BiocGenerics:::testPackage("DelayedArray")

Attaching package: 'genefilter'

The following objects are masked from 'package:MatrixGenerics':

    rowSds, rowVars

The following objects are masked from 'package:matrixStats':

    rowSds, rowVars

Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
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, 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: 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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum, scale, sweep

Loading required package: rhdf5

Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls


Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
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, 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: 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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum, scale, sweep

Loading required package: rhdf5

Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls


Timing stopped at: 1.593 0.035 11.03
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': file '/tmp/Rtmp1ZwqFR/HDF5Array_dump/auto00001.h5' does not exist
In addition: Warning messages:
1: In log(a + 0.2) : NaNs produced
2: In OP(a) : NaNs produced
3: Argument 'center' should be of the same length as number of rows of 'x'. Use of a scalar value is deprecated: 1 != 8 
4: Argument 'center' should be of the same length as number of rows of 'x'. Use of a scalar value is deprecated: 1 != 8 
5: Argument 'center' should be of the same length as number of rows of 'x'. Use of a scalar value is deprecated: 1 != 8 
Error in normarg_perm(perm, dim(seed)) : 'perm' must be an integer vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    'perm' cannot be an empty vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions equal to 1 can be dropped
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    all non-NA values in 'perm' must be >= 1 and <= 'length(dim(a))'
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions equal to 1 can be dropped
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in match.fun(OP) : 'NULL' is not a function, character or symbol
Error in match.fun(OP) : 
  'list(NULL)' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'not-an-existing-function' of mode 'function' was not found
Error in new_DelayedNaryIsoOp("<=", array(dim = 4:2), array(dim = 2:4)) : 
  non-conformable array-like objects
Error in normarg_dimnames(dimnames, seed_dim) : 
  the supplied 'dimnames' must be NULL or a list
Error in normarg_dimnames(dimnames, seed_dim) : 
  the supplied 'dimnames' must have one list element per dimension
Error in FUN(X[[i]], ...) : 
  each list element in the supplied 'dimnames' must be NULL or a
  character vector
Error in FUN(X[[i]], ...) : 
  length of 'dimnames[[1]]' (26) must equal the array extent (5)
Error in normalizeNindex(Nindex, seed) : 
  'Nindex' must be a list with one list element per dimension in 'x'
Error in normalizeNindex(Nindex, seed) : 
  'Nindex' must be a list with one list element per dimension in 'x'
Error : subscript contains out-of-bounds indices
Error : subscript contains invalid names
Error : subscript contains out-of-bounds ranges
Error : subscript contains out-of-bounds ranges
Error in new_DelayedUnaryIsoOpStack(.TEST_SAS3, NULL) : 
  'OPS' must be a list
Error in FUN(X[[i]], ...) : 
  'OPS[[1L]]' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'not-an-existing-function' of mode 'function' was not found


RUNIT TEST PROTOCOL -- Sat Oct 15 08:30:03 2022 
*********************************************** 
Number of test functions: 55 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
DelayedArray RUnit Tests - 55 test functions, 1 error, 0 failures
ERROR in test_DelayedMatrix_mult_parallel: Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': file '/tmp/Rtmp1ZwqFR/HDF5Array_dump/auto00001.h5' does not exist

Test files with failing tests

   test_DelayedMatrix-utils.R 
     test_DelayedMatrix_mult_parallel 


Error in BiocGenerics:::testPackage("DelayedArray") : 
  unit tests failed for package DelayedArray
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no HDF5Array_1.24.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/HDF5Array.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.24.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HDF5Array’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs      9.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
':::' call which should be '::': ‘rhdf5:::H5Fclose’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘S4Vectors:::anyMissingOrOutside’
  ‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::sapply_isNULL’
  ‘rhdf5:::h5checktypeOrOpenLocS3’
  See the note in ?`:::` about the use of this operator.
* 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 ... SKIPPED
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘run_longtests.R’
 ERROR
Running the tests in ‘longtests/run_longtests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  DelayedArray RUnit Tests - 55 test functions, 1 error, 0 failures
  ERROR in test_DelayedMatrix_mult_parallel: Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'as.matrix': file '/tmp/Rtmp1ZwqFR/HDF5Array_dump/auto00001.h5' does not exist
  
  Test files with failing tests
  
     test_DelayedMatrix-utils.R 
       test_DelayedMatrix_mult_parallel 
  
  
  Error in BiocGenerics:::testPackage("DelayedArray") : 
    unit tests failed for package DelayedArray
  Execution halted
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/HDF5Array.Rcheck/00check.log’
for details.

* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5File.c -o H5File.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c global_errmsg_buf.c -o global_errmsg_buf.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5DSetDescriptor.c -o H5DSetDescriptor.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5dimscales.c -o h5dimscales.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c uaselection.c -o uaselection.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5mread_helpers.c -o h5mread_helpers.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5mread_startscounts.c -o h5mread_startscounts.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ChunkIterator.c -o ChunkIterator.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5mread_index.c -o h5mread_index.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:206:13: warning: ‘NOT_USED_make_nzindex_from_bufs’ defined but not used [-Wunused-function]
  206 | static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:179:13: warning: ‘NOT_USED_make_nzdata_from_IntAE_bufs’ defined but not used [-Wunused-function]
  179 | static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:123:13: warning: ‘NOT_USED_make_nzindex_from_buf’ defined but not used [-Wunused-function]
  123 | static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5mread.c -o h5mread.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5summarize.c -o h5summarize.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc-longtests/meat/HDF5Array.Rcheck/00LOCK-HDF5Array/00new/HDF5Array/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (HDF5Array)