Long tests report for BioC 3.9 - CHECK report for HDF5Array on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-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_1.12.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc-longtests/meat/HDF5Array.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.2’
* 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 ... ERROR
Installation failed.
See ‘/home/biocbuild/bbs-3.9-bioc-longtests/meat/HDF5Array.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc-longtests/meat/HDF5Array.Rcheck/00check.log’
for details.

* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c DSet.c -o DSet.o
DSet.c: In function ‘_get_DSet’:
DSet.c:100:6: warning: ‘storage_mode_attr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (strcmp(storage_mode, "integer") == 0) {
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DSet.c:210:8: note: ‘storage_mode_attr’ was declared here
  char *storage_mode_attr;
        ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c array_selection.c -o array_selection.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c h5mread.c -o h5mread.o
h5mread.c:1194:22: warning: ‘select_elements_from_chunk’ defined but not used [-Wunused-function]
 static long long int select_elements_from_chunk(const DSet *dset,
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o HDF5Array.so DSet.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o "/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libhdf5.a" "/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libsz.a" -lz -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
gcc: error: "/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libhdf5.a": No such file or directory
gcc: error: "/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libsz.a": No such file or directory
/home/biocbuild/bbs-3.9-bioc/R/share/make/shlib.mk:6: recipe for target 'HDF5Array.so' failed
make: *** [HDF5Array.so] Error 1
ERROR: compilation failed for package ‘HDF5Array’
* removing ‘/home/biocbuild/bbs-3.9-bioc-longtests/meat/HDF5Array.Rcheck/HDF5Array’

CHECK report for HDF5Array on malbec2

Summary

Tests output

'R CMD check' output

Installation output